diff --git a/mkdocs.yml b/mkdocs.yml
index 28ba5d5b5a..0f5a1691fb 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -10,6 +10,7 @@ nav:
           - Data summary files: modality-agnostic-files/data-summary-files.md
           - Phenotypic and assessment data: modality-agnostic-files/phenotypic-and-assessment-data.md
           - Code: modality-agnostic-files/code.md
+          - Provenance: modality-agnostic-files/provenance.md
           - Events: modality-agnostic-files/events.md
       - Modality specific files:
           - Magnetic Resonance Imaging: modality-specific-files/magnetic-resonance-imaging-data.md
@@ -120,6 +121,9 @@ markdown_extensions:
         - name: tsvgz
           class: tsv
           format: !!python/name:bidsschematools.render.tsv.fence
+        - name: mermaid
+          class: mermaid
+          format: !!python/name:pymdownx.superfences.fence_code_format
   - admonition
   - pymdownx.details
 plugins:
diff --git a/src/common-principles.md b/src/common-principles.md
index c3a395c600..6a72e3dfc2 100644
--- a/src/common-principles.md
+++ b/src/common-principles.md
@@ -928,10 +928,10 @@ Bare DOIs such as `10.18112/openneuro.ds000001.v1.0.0` are [DEPRECATED][].
 
 ### BIDS URI
 
-To reference files in BIDS datasets, the following URI scheme may be used:
+To reference files or directories in BIDS datasets, the following URI scheme may be used:
 
 ```plain
-bids:[<dataset-name>]:<relative-path>
+bids:[<dataset-name>]:<relative-path>[#<fragment>]
 ```
 
 The scheme component `bids` identifies a BIDS URI,
@@ -940,6 +940,7 @@ The `dataset-name` component is an identifier for a BIDS dataset,
 and the `relative-path` component is the location of a resource within that
 BIDS dataset, relative to the root of that dataset.
 The `relative-path` MUST NOT start with a forward-slash character (`/`).
+The `fragment` MAY be used to identify a resource that is subordinate to the file or directory.
 
 Examples:
 
@@ -947,11 +948,16 @@ Examples:
 bids::sub-01/fmap/sub-01_dir-AP_epi.nii.gz
 bids:ds000001:sub-02/anat/sub-02_T1w.nii.gz
 bids:myderivatives:sub-03/func/sub-03_task-rest_space-MNI152_bold.nii.gz
+bids:fmriprep:sub-001/anat/sub-001_T1w_preproc.nii.gz#aa56ztg8
+bids::prov#preprocessing-00f3a18f
 ```
 
 If no dataset name is specified, the URI is relative to the current BIDS dataset.
 This is made more precise in the next section.
 
+!!! note
+    A BIDS dataset can be referenced using the BIDS URI of its root directory. For example: `bids:ds000001:.`
+
 #### Resolution of BIDS URIs
 
 In order to resolve a BIDS URI, the dataset name must be mapped to a BIDS dataset.
@@ -1003,7 +1009,7 @@ No protocol is currently proposed to automatically resolve all possible BIDS URI
 
 BIDS URIs are parsable as standard [URIs][] with scheme `bids` and path
 `[<dataset-name>]:<relative-path>`.
-The authority, query and fragment components are unused.
+The authority and query components are unused.
 Future versions of BIDS may specify interpretations for these components,
 but MUST NOT change the interpretation of a previously valid BIDS URI.
 For example, a future version may specify an authority that would allow BIDS
diff --git a/src/introduction.md b/src/introduction.md
index 2a5a377fe7..f0070de928 100644
--- a/src/introduction.md
+++ b/src/introduction.md
@@ -192,6 +192,15 @@ For example:
     Scientific Data 12, (13841).
     [doi:10.1038/s41597-025-05543-2](https://doi.org/10.1038/s41597-025-05543-2)
 
+### Other extensions specific publications
+
+#### Provenance
+
+-   Rémi Adon, Stefan Appelhoff, Tibor Auer, Laurent Guillo, Yaroslav O Halchenko, David Keator, Christopher J Markiewicz, Thomas E Nichols, Jean-Baptiste Poline, Satrajit Ghosh, Camille Maumet (2021).
+    **BIDS-prov: a provenance framework for BIDS**.
+    OHBM 2021 - 25th Annual Meeting of the Organization for Human Brain Mapping, Jun 2021, Online, South Korea. pp.1-3
+    [https://inserm.hal.science/inserm-03478998v1](https://inserm.hal.science/inserm-03478998v1)
+
 ### Research Resource Identifier (RRID)
 
 BIDS has also a
diff --git a/src/metaschema.json b/src/metaschema.json
index e5d4c7b400..ea06b89fa0 100644
--- a/src/metaschema.json
+++ b/src/metaschema.json
@@ -359,6 +359,15 @@
                   },
                   "additionalProperties": false
                 },
+                "modality_agnostic": {
+                  "type": "object",
+                  "patternProperties": {
+                    "^[a-zA-Z0-9_]+$": {
+                      "$ref": "#/definitions/suffixRule"
+                    }
+                  },
+                  "additionalProperties": false
+                },
                 "tables": {
                   "type": "object",
                   "patternProperties": {
@@ -372,7 +381,7 @@
                   "additionalProperties": false
                 }
               },
-              "required": ["core", "tables"],
+              "required": ["core", "modality_agnostic", "tables"],
               "additionalProperties": false
             },
             "deriv": {
diff --git a/src/modality-agnostic-files/dataset-description.md b/src/modality-agnostic-files/dataset-description.md
index 79d75264c3..c4f45f259c 100644
--- a/src/modality-agnostic-files/dataset-description.md
+++ b/src/modality-agnostic-files/dataset-description.md
@@ -45,16 +45,9 @@ and a guide for using macros can be found at
    }
 ) }}
 
-Each object in the `GeneratedBy` array includes the following REQUIRED, RECOMMENDED
-and OPTIONAL keys:
-
-<!-- This block generates a table describing subfields within a metadata field.
-The definitions of these fields can be found in
-  src/schema/objects/metadata.yaml
-and a guide for using macros can be found at
- https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
--->
-{{ MACROS___make_subobject_table("metadata.GeneratedBy.items") }}
+!!! Note
+    See the [Provenance of a BIDS dataset](provenance.md#provenance-of-a-bids-dataset) section
+    for more information on how to describe provenance using the `GeneratedBy` field.
 
 Example:
 
@@ -107,8 +100,6 @@ Example:
 }
 ```
 
-### Derived dataset and pipeline description
-
 As for any BIDS dataset, a `dataset_description.json` file MUST be found at the
 top level of every derived dataset:
 `<dataset>/derivatives/<pipeline-name>/dataset_description.json`.
diff --git a/src/modality-agnostic-files/provenance.md b/src/modality-agnostic-files/provenance.md
new file mode 100644
index 0000000000..18d6cb166a
--- /dev/null
+++ b/src/modality-agnostic-files/provenance.md
@@ -0,0 +1,774 @@
+# Provenance
+
+Support for provenance was developed as a [BIDS Extension Proposal](../extensions.md#bids-extension-proposals).
+Please see [Citing BIDS](../introduction.md#citing-bids) on how to appropriately credit this extension when referring to it in the
+context of the academic literature.
+
+!!! bug
+    Change example links below once they are merged to bids-examples
+
+!!! example "Example datasets"
+
+    The following examples have been formatted using this specification
+    and can be used for practical guidance when curating a new dataset.
+
+    - [Provenance of DICOM to Nifti conversion with `dcm2niix`](https://github.com/bclenet/bids-examples/tree/BEP028_dcm2niix/provenance_dcm2niix) - [Associated Pull Request #494](https://github.com/bids-standard/bids-examples/pull/494)
+    - [Provenance of DICOM to Nifti conversion with `heudiconv`](https://github.com/bclenet/bids-examples/tree/BEP028_heudiconv/provenance_heudiconv) - [Associated Pull Request #496](https://github.com/bids-standard/bids-examples/pull/496)
+    - [Provenance of fMRI preprocessing with `SPM`](https://github.com/bclenet/bids-examples/tree/BEP028_spm/provenance_spm) - [Associated Pull Request #497](https://github.com/bids-standard/bids-examples/pull/497)
+    - [Provenance of fMRI preprocessing with `fMRIPrep`](https://github.com/bclenet/bids-examples/tree/BEP028_fmriprep/provenance_fmriprep) - [Associated Pull Request#502](https://github.com/bids-standard/bids-examples/pull/502)
+
+    Further datasets are available from
+    the [BIDS examples repository](https://bids-website.readthedocs.io/en/latest/datasets/examples.html#provenance).
+
+## Overview
+
+This part of the BIDS specification is aimed at describing the provenance of a BIDS dataset.
+
+This description is retrospective: it describes a set of steps that were executed in order to obtain the dataset.
+
+!!! note
+    This is different from prospective provenance that focuses describing workflows that may be run on a dataset.
+
+This description is based on the [W3C Prov](https://www.w3.org/TR/2013/REC-prov-o-20130430/) standard.
+
+### General principles
+
+Provenance information SHOULD be included in a BIDS dataset when possible.
+
+If provenance information is included, it MUST be described using the conventions detailed by this specification.
+
+Provenance information reflects the provenance of a full dataset and/or of specific files at any level of the BIDS hierarchy.
+
+Provenance information SHOULD not include human subject identifying data.
+
+### Key concepts
+
+Provenance information is encoded using metadata fields.
+
+For the most part, this metadata consists of **provenance objects** of 4 types:
+
+-   **Activities**: transformations that have been applied to data.
+-   **ProvEntities**: input or output data for activities (Note: this corresponds to Entities as per the Prov W3C standard, the prefix "Prov" is used to disambiguate with [BIDS entities](../appendices/entities.md)).
+-   **Software**: software packages used to compute the activities.
+-   **Environments**: software environments in which activities were performed.
+
+!!! example "Minimal provenance example"
+
+    ```mermaid
+    flowchart BT
+        B[Brain extraction] -->|wasAssociatedWith| S{FSL<br>}
+        B -->|used| T1([sub-001_T1w.nii])
+        B -->|used| L((Linux))
+        T1p([sub-001_T1w_preproc.nii]) -->|wasGeneratedBy| B
+    ```
+
+    In this example, a brain extraction algorithm was applied on a T1-weighted image:
+
+    - *sub-001_T1w.nii* is the original T1-weighted image;
+    - *sub-001_T1w_preproc.nii* is the skull striped image;
+    - the *"Brain extraction"* activity was performed using the *FSL* software within a *Linux* software environment.
+
+Provenance objects are described as JSON objects in BIDS. They are stored inside **provenance files** (see [Provenance files](#provenance-files)). Additionally, metadata of provEntities can be stored as BIDS metadata inside sidecar JSON files (see [Provenance of a BIDS file](#provenance-of-a-bids-file)) as well as in `dataset_description.json` files (see [Provenance of a BIDS dataset](#provenance-of-a-bids-dataset)).
+
+## Provenance files
+
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the directory
+  src/schema/rules/files/common
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_filename_template(
+   "common",
+   datatypes=["prov"],
+   suffixes=["act", "ent", "env", "soft"])
+}}
+
+!!! note
+    The `prov` BIDS entity allows to group related provenance files, using an arbitrary value for `<label>`. A subdirectory MAY be used to group provenance files sharing the same `prov` entity.
+
+The following suffixes specify the contents of provenance files.
+
+<!--
+This block generates a suffix table.
+The definitions of these fields can be found in
+  src/schema/objects/suffixes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_suffix_table(
+      ["act", "ent", "env", "soft"]
+   )
+}}
+
+!!! example "Example of organization for provenance files"
+    ```
+    prov/
+    ├─ prov-preprocspm/
+    │  ├─ prov-preprocspm_desc-v1_act.json
+    │  ├─ prov-preprocspm_desc-v1_ent.json
+    │  ├─ prov-preprocspm_desc-v2_act.json
+    │  └─ prov-preprocspm_desc-v2_ent.json
+    ├─ prov-preprocfsl_act.json
+    ├─ prov-preprocfsl_ent.json
+    ├─ prov-preprocfsl_env.json
+    ├─ prov-preprocfsl_soft.json
+    └─ ...
+    ```
+
+### Provenance description file
+
+Template:
+
+```text
+prov/
+    provenance.tsv
+    provenance.json
+```
+
+The purpose of this RECOMMENDED file is to describe properties of provenance files. It MUST contain the column `provenance_label`, which MUST consist of `prov-<label>` values identifying one row for each `prov` entity in the dataset, followed by an optional column containing a description for the entity. Each entity MUST be described by one and only one row.
+
+We RECOMMEND to make use of these columns, and
+in case that you do use them, we RECOMMEND to use the following values
+for them:
+
+<!-- This block generates a columns table.
+The definitions of these fields can be found in
+  src/schema/rules/tabular_data/*.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_columns_table("modality_agnostic.Provenance") }}
+
+Throughout BIDS you can indicate missing values with `n/a` (for "not
+available").
+
+`provenance.tsv` example:
+
+```tsv
+provenance_label	description
+prov-preprocspm	Provenance of preprocessing performed with SPM.
+prov-preprocfsl	Provenance of preprocessing performed with FSL.
+```
+
+It is RECOMMENDED to accompany each `provenance.tsv` file with a sidecar
+`provenance.json` file to describe the TSV column names and properties of their values
+(see also the [section on tabular files](../common-principles.md#tabular-files)).
+
+`provenance.json` example:
+
+```JSON
+{
+    "description": {
+        "Description": "Description of the provenance file(s)."
+    }
+}
+```
+
+### Activities
+
+Each file with a `act` suffix is a JSON file describing activities.
+
+Each file MUST include the following key:
+
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_metadata_table(
+   {
+      "Activities": "REQUIRED"
+   }
+) }}
+
+Each object in the `Activities` array includes the following keys:
+
+<!-- This block generates a table describing subfields within a metadata field.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_subobject_table("metadata.Activities.items") }}
+
+!!! example "Example: a provenance object in a `prov/[<subdir>/]prov-<label>_act.json` file"
+    ```JSON
+    {
+        "Activities": [
+            {
+                "Id": "bids::prov#conversion-00f3a18f",
+                "Label": "Dicom to Nifti conversion",
+                "Command": "dcm2niix -o . -f sub-%i/anat/sub-%i_T1w sourcedata/dicoms",
+                "AssociatedWith": "bids::prov#dcm2niix-khhkm7u1",
+                "Used": [
+                    "bids::prov#fedora-uldfv058",
+                    "bids::sourcedata/dicoms"
+                ],
+                "StartedAtTime": "2025-03-13T10:26:00",
+                "EndedAtTime": "2025-03-13T10:26:05"
+            }
+        ]
+    }
+    ```
+    This snippet is similar to Activities described in the [DICOM to Nifti conversion with `dcm2niix` example](https://github.com/bclenet/bids-examples/tree/BEP028_dcm2niix/provenance_dcm2niix).
+
+### ProvEntities
+
+Each file with a `ent` suffix is a JSON file describing provEntities.
+
+!!! warning
+    These files SHOULD not contain provEntities describing data files that are available in the dataset. Use sidecar JSON files instead for this purpose (see [Provenance of a BIDS file](#provenance-of-a-bids-file)).
+
+    These files SHOULD not contain provEntities describing the current dataset. Use `dataset_description.json` files instead for this purpose (see [Provenance of a BIDS dataset](#provenance-of-a-bids-dataset)).
+
+Each file MUST include the following key:
+
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_metadata_table(
+   {
+      "ProvEntities": "REQUIRED"
+   }
+) }}
+
+Each object in the `ProvEntities` array includes the following keys:
+
+<!-- This block generates a table describing subfields within a metadata field.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_subobject_table("metadata.ProvEntities.items") }}
+
+!!! example "Example: a provenance object in a `prov/[<subdir>/]prov-<label>_ent.json` file"
+    ```JSON
+    {
+        "ProvEntities": [
+            {
+                "Id": "bids::sub-01/func/sub-01_task-tonecounting_bold.nii",
+                "Label": "sub-01_task-tonecounting_bold.nii",
+                "AtLocation": "sub-01/func/sub-01_task-tonecounting_bold.nii",
+                "GeneratedBy": "bids::prov#realign-acea8093",
+                "Digest": {
+                    "sha256": "a4e801438b9c36df010309c94fc4ef8b07d95e7d9cb2edb8c212a5e5efc78d90"
+                }
+            }
+        ]
+    }
+    ```
+    This is a snippet from the [fMRI preprocessing with `SPM` example](https://github.com/bclenet/bids-examples/tree/BEP028_spm/provenance_spm)
+
+### Software
+
+Each file with a `soft` suffix is a JSON file describing software.
+
+Each file MUST include the following key:
+
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_metadata_table(
+   {
+      "Software": "REQUIRED"
+   }
+) }}
+
+Each object in the `Software` array includes the following keys:
+
+<!-- This block generates a table describing subfields within a metadata field.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_subobject_table("metadata.Software.items") }}
+
+!!! example "Example: a provenance object in a `prov/[<subdir>/]prov-<label>_soft.json` file"
+    ```JSON
+    {
+        "Software": [
+            {
+                "Id": "bids::prov#dcm2niix-khhkm7u1",
+                "AltIdentifier": "RRID:SCR_023517",
+                "Label": "dcm2niix",
+                "Version": "v1.0.20220720"
+            }
+        ]
+    }
+    ```
+    This is a snippet from the [DICOM to Nifti conversion with `dcm2niix` example](https://github.com/bclenet/bids-examples/tree/BEP028_dcm2niix/provenance_dcm2niix)
+
+### Environments
+
+Each file with a `env` suffix is a JSON file describing environments.
+
+Each file MUST include the following key:
+
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_metadata_table(
+   {
+      "Environments": "REQUIRED"
+   }
+) }}
+
+Each object in the `Environments` array includes the following keys:
+
+<!-- This block generates a table describing subfields within a metadata field.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_subobject_table("metadata.Environments.items") }}
+
+!!! example "Example: a provenance object in a `prov/[<subdir>/]prov-<label>_env.json` file"
+    ```JSON
+    {
+        "Environments": [
+            {
+                "Id": "bids::prov#fedora-uldfv058",
+                "Label": "Fedora release 36 (Thirty Six)",
+                "OperatingSystem": "GNU/Linux 6.2.15-100.fc36.x86_64"
+            }
+        ]
+    }
+    ```
+    This is a snippet from the [DICOM to Nifti conversion with `dcm2niix` example](https://github.com/bclenet/bids-examples/tree/BEP028_dcm2niix/provenance_dcm2niix)
+
+## Provenance of a BIDS file
+
+Metadata of a provEntity describing a BIDS file SHOULD be stored inside its sidecar JSON.
+
+Any sidecar JSON file MAY include the following keys:
+
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_metadata_table(
+   {
+      "GeneratedById": "OPTIONAL",
+      "SidecarGeneratedBy": "OPTIONAL",
+      "Digest": "OPTIONAL",
+      "ProvEntityType": "OPTIONAL"
+   }
+) }}
+
+!!! example "Example of metadata in a sidecar JSON file"
+    ```JSON
+    {
+        "GeneratedBy": "bids::prov#conversion-00f3a18f",
+        "SidecarGeneratedBy": [
+            "bids::prov#preparation-conversion-1xkhm1ft",
+            "bids::prov#conversion-00f3a18f"
+        ],
+        "Digest": {
+            "sha256": "66eeafb465559148e0222d4079558a8354eb09b9efabcc47cd5b8af6eed51907"
+        }
+    }
+    ```
+    This snippet is similar to fields described in [DICOM to Nifti conversion with `heudiconv` example](https://github.com/bclenet/bids-examples/tree/BEP028_heudiconv/provenance_heudiconv).
+
+## Provenance of a BIDS dataset
+
+Metadata of a provEntity describing a BIDS dataset (raw, derivative, or study) SHOULD be stored inside its `dataset_description.json` file. This metadata describes the provenance of the whole dataset.
+
+The `dataset_description.json` file of a **BIDS raw dataset** or **BIDS study dataset** MAY include the `GeneratedBy` key to describe provenance.
+
+The `dataset_description.json` file of a **BIDS derivative dataset** MUST include the `GeneratedBy` key to describe provenance.
+
+The `GeneratedBy` field MAY contain either of the following values:
+
+-   Identifier(s) of the activity (one or more) responsible for the creation of the dataset (see the [Description using provenance objects](#description-using-provenance-objects) section).
+-   A description of pipelines or processes responsible for the creation of the dataset (see the [Description of pipelines or processes](#description-of-pipelines-or-processes) section).
+
+### Description using provenance objects
+
+This section details the way to describe provenance of a dataset in the `GeneratedBy` field, using provenance objects.
+
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_metadata_table(
+   {
+      "GeneratedById": "RECOMMENDED for BIDS raw datasets and BIDS study datasets, REQUIRED for BIDS derivative datasets"
+   }
+) }}
+
+!!! example "Example of `GeneratedBy` contents in a `dataset_description.json`"
+    ```JSON
+    {
+        "GeneratedBy": "bids::prov#preprocessing-xMpFqB5q"
+    }
+    ```
+    This is a snippet from the [fMRI preprocessing with `fMRIPrep` example](https://github.com/bclenet/bids-examples/tree/BEP028_fmriprep/provenance_fmriprep).
+
+### Description of processes or pipelines
+
+This section details a way to describe the provenance of a dataset, providing `GeneratedBy` with an array of objects representing pipelines or processes that generated the dataset.
+
+!!! note
+    This description can be equivalently represented using the previous section. This modeling is kept for backward-compatibility but might be removed in future BIDS releases (see BIDS 2.0).
+
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_metadata_table(
+   {
+      "GeneratedBy": "RECOMMENDED for BIDS raw datasets and BIDS study datasets, REQUIRED for BIDS derivative datasets"
+   }
+) }}
+
+Each object in the `GeneratedBy` array includes the following REQUIRED, RECOMMENDED
+and OPTIONAL keys:
+
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_metadata_table(
+   {
+      "Name__GeneratedBy": "REQUIRED",
+      "Version__GeneratedBy": "RECOMMENDED",
+      "Description__GeneratedBy": 'RECOMMENDED if `Name` is `"Manual"`, OPTIONAL otherwise',
+      "CodeURL": "OPTIONAL",
+      "Container": "OPTIONAL"
+   }
+) }}
+
+!!! example "Example of `GeneratedBy` contents in a `dataset_description.json`"
+    ```JSON
+    {
+        "GeneratedBy": [
+            {
+              "Name": "reproin",
+              "Version": "0.6.0",
+              "Container": {
+                "Type": "docker",
+                "Tag": "repronim/reproin:0.6.0"
+              }
+            }
+        ]
+    }
+    ```
+
+## Consistency and uniqueness of identifiers
+
+The following rules and conventions are provided in order to have consistent, human readable, and explicit [IRIs](https://www.w3.org/TR/json-ld11/#iris) as identifiers for provenance objects.
+
+!!! note
+    The `Id` field contains the identifier of a provenance objects.
+
+### Identifiers for provEntities
+
+The identifier of a provEntity describing a BIDS file SHOULD be a [BIDS URI](../common-principles.md#bids-uri).
+
+!!! warning
+    The use of BIDS URIs may require to define the `DatasetLinks` object in [`dataset_description.json`](dataset-description.md#dataset_descriptionjson).
+
+In other cases, the identifier of a provEntity described in a BIDS dataset `<dataset-name>` SHOULD have the following form, where `<label>` is an arbitrary value for identifying the provEntity.
+
+```text
+bids:[<dataset-name>]:prov#provEntity-<label>
+```
+
+!!! example "Examples of identifiers for provEntities"
+    - `bids:ds001734:sub-002/anat/sub-02_T1w.nii` - a provEntity describing a T1w file for subject `sub-002` in the `ds001734` dataset;
+    - `bids::sub-014/func/sub-014_task-MGT_run-01_events.tsv` - a provEntity describing an events file for subject `sub-014` in the current dataset;
+    - `bids:fmriprep:sub-001/func/sub-001_task-MGT_run-01_bold_space-MNI152NLin2009cAsym_preproc.nii.gz` - a provEntity describing a bold file for subject `sub-001` in the `fmriprep` dataset;
+    - `bids::prov#provEntity-acea8093` - a provEntity describing a file that is not available in the dataset.
+
+### Identifiers for other provenance objects
+
+The identifier of an activity, software, or environment described in a BIDS dataset `<dataset-name>` SHOULD have the following form, where `<label>` is a human readable name for coherently identifying the provenance objects and `<uid>` is a unique group of chars.
+
+```text
+bids:[<dataset-name>]:prov#<label>-<uid>
+```
+
+The uniqueness of this identifier MUST be used to distinguish any activity, software, or environment that are different in any of their attributes.
+
+!!! example "Examples of identifiers for activities, environments and software"
+    - `bids:ds001734:prov#conversion-xfMMbHK1` - a conversion activity described inside the `ds001734` dataset;
+    - `bids::prov#fedora-uldfv058` - a Fedora based environment described inside the current dataset.
+    - `bids:preprocessing:prov#fmriprep-r4kzzMt8` - the fMRIPrep software described inside the `preprocessing` dataset.
+
+## BIDS provenance from a RDF perspective
+
+The Resource Description Framework (RDF) is a method to describe and exchange graph data.
+
+The terms defined in this part of the BIDS specification are based on the [W3C Prov](https://www.w3.org/TR/2013/REC-prov-o-20130430/) standard. Their relations with W3C Prov terms are defined in the [`provenance-context.json`]() file.
+
+Provenance metadata can be aggregated into JSON-LD files that represent RDF graphs.
+
+Insert examples and links to bids-examples here.
+
+## Minimal examples
+
+### Provenance of a BIDS raw dataset
+
+!!! example
+    This section shows a snippet from the [Provenance of DICOM to Nifti conversion with `dcm2niix`](https://github.com/bclenet/bids-examples/tree/BEP028_dcm2niix/provenance_dcm2niix) example.
+
+In this example, we explain provenance metadata of a DICOM to Nifti conversion with `dcm2niix`. Consider the following BIDS raw dataset:
+
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_filetree_example(
+    {
+        "prov": {
+            "prov-dcm2niix_act.json": "",
+            "prov-dcm2niix_soft.json": "",
+            "...": ""
+        },
+        "sourcedata": {
+            "dicoms": {
+                "...": "",
+            },
+        },
+        "sub-001": {
+            "anat": {
+                "sub-001_T1w.json": "",
+                "sub-001_T1w.nii.gz": ""
+            },
+        },
+        "...": ""
+    }
+) }}
+
+The `prov/prov-dcm2niix_soft.json` file describes `dcm2niix`, the software package used for the DICOM conversion. As per the [Consistency and uniqueness of identifiers](#consistency-and-uniqueness-of-identifiers) section, the identifier for the associated software provenance object SHOULD start with `bids:<dataset>:prov#` (`bids::` refers to the current dataset).
+
+```JSON
+{
+  "Software": [
+    {
+      "Id": "bids::prov#dcm2niix-khhkm7u1",
+      "Label": "dcm2niix",
+      ...
+    }
+  ]
+}
+```
+
+The `prov/prov-dcm2niix_act.json` file describes the conversion activity. Note that the identifier of the previously described software package is used here to describe that the software package was used to compute this activity.
+
+```JSON
+{
+    "Activities": [
+        {
+            "Id": "bids::prov#conversion-00f3a18f",
+            "Label": "Conversion",
+            "AssociatedWith": "bids::prov#dcm2niix-khhkm7u1",
+            ...
+        }
+    ]
+}
+```
+
+Inside the `sub-001/anat/sub-001_T1w.json` file, the metadata field `GeneratedBy` indicates that the `sub-001/anat/sub-001_T1w.nii.gz` file was generated by the previously described activity.
+
+```JSON
+{
+    ...
+    "GeneratedBy": "bids::prov#conversion-00f3a18f",
+    ...
+}
+```
+
+### Provenance of a BIDS derivative dataset
+
+!!! example
+    This section shows a snippet from the [Provenance of fMRI preprocessing with `SPM`](https://github.com/bclenet/bids-examples/tree/BEP028_spm/provenance_spm) example.
+
+In this example, we explain provenance metadata of fMRI preprocessing steps performed with `SPM`. Consider the following BIDS derivative dataset:
+
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_filetree_example(
+    {
+        "prov": {
+            "prov-spm_act.json": "",
+            "prov-spm_ent.json": "",
+            "...": ""
+        },
+        "sub-01": {
+            "anat": {
+                "c1sub-001_T1w.json": "",
+                "c1sub-001_T1w.nii": "",
+                "...": "",
+                "sub-001_T1w.json": "",
+                "sub-001_T1w.nii": "",
+                "...": ""
+            },
+            "func": {
+                "...": ""
+            }
+        },
+        "...": ""
+    }
+) }}
+
+The `prov/prov-spm_act.json` file describes the preprocessing steps as activities provenance objects. Among them:
+
+-   the `bids::prov#movefile-bac3f385` activity used a T1w file from the ds000011 dataset;
+-   the brain segmentation -identified by `bids::prov#segment-7d5d4ac5`- needed two files listed as provEntities inside the `Used` array.
+
+```JSON
+{
+    "Activities": [
+        {
+            "Id": "bids::prov#movefile-bac3f385",
+            "Label": "Move file",
+            "Used": [
+                "bids:ds000011:sub-01/anat/sub-01_T1w.nii.gz"
+            ],
+            ...
+        },
+        ...
+        {
+            "Id": "bids::prov#segment-7d5d4ac5",
+            "Label": "Segment",
+            "Used": [
+                "urn:c1d082a5-34ee-4282-99df-28c0ba289210",
+                "bids::sub-01/anat/sub-01_T1w.nii"
+            ],
+            ...
+        },
+        ...
+    ]
+}
+```
+
+The BIDS file described by provEntity `bids::sub-01/anat/sub-01_T1w.nii` is available in the current dataset. The file described by provEntity `urn:c1d082a5-34ee-4282-99df-28c0ba289210` is not inside the dataset. The provEntity is stored inside `prov/prov-spm_ent.json`:
+
+```JSON
+{
+    "ProvEntities": [
+        ...
+        {
+          "Id": "urn:c1d082a5-34ee-4282-99df-28c0ba289210",
+          "Label": "TPM.nii",
+          "AtLocation": "spm12/tpm/TPM.nii",
+          ...
+        },
+        ...
+    ]
+}
+```
+
+Inside the `sub-001/anat/c1sub-001_T1w.json` file, the metadata field `GeneratedBy` indicates that the `c1sub-001/anat/sub-001_T1w.nii.gz` file was generated by the previously described brain segmentation activity.
+
+```JSON
+{
+    "GeneratedBy": "bids::prov#segment-7d5d4ac5",
+    ...
+}
+```
+
+### Provenance of a BIDS study dataset
+
+In this example, we explain provenance metadata of fMRI preprocessing steps performed with `fMRIPrep`. Consider the following BIDS study dataset:
+
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_filetree_example(
+    {
+        "dataset_description.json": "",
+        "derivatives": {
+            "fmriprep": {
+                "sub-01": {},
+                "sub-02": {},
+                "...": ""
+            }
+        },
+        "prov": {
+            "prov-fmriprep_act.json": "",
+            "prov-fmriprep_ent.json": ""
+        },
+        "sourcedata": {
+            "raw": {
+                "sub-01": {},
+                "sub-02": {},
+                "...": ""
+            }
+        },
+        "...": ""
+   }
+) }}
+
+Inside the `dataset_description.json` file of the study dataset, dataset names are defined in the `DatasetLinks` metadata field in order to refer to two nested datasets using BIDS URIs.
+
+```JSON
+{
+    ...
+    "DatasetLinks": {
+        "raw": "sourcedata/raw",
+        "fmriprep": "derivatives/fmriprep"
+    }
+}
+```
+
+The `prov/prov-fmriprep_ent.json` file describes two provEntities: one per nested dataset.
+
+```JSON
+{
+    "ProvEntities": [
+        {
+            "Id": "bids:raw:.",
+            "Label": "Raw data"
+        },
+        {
+            "Id": "bids:fmriprep:.",
+            "Label": "Preprocessed data",
+            "GeneratedBy": "bids::prov#preprocessing-00f3a18f"
+        },
+    ]
+}
+```
+
+The `prov/prov-fmriprep_act.json` file describes the activity that generated the derivative dataset using the raw dataset.
+
+```JSON
+{
+    "Activities": [
+        {
+            "Id": "bids::prov#preprocessing-00f3a18f",
+            "Label": "Preprocessing with fMRIprep",
+            "Command": "docker run  -v sourcedata/raw:/data:ro -v derivatives/fmriprep:/out poldracklab/fmriprep:1.1.4 /data /out",
+            "Used": "bids:raw:."
+        }
+    ]
+}
+```
diff --git a/src/provenance-context.json b/src/provenance-context.json
new file mode 100644
index 0000000000..18238b758c
--- /dev/null
+++ b/src/provenance-context.json
@@ -0,0 +1,52 @@
+{
+    "@context": {
+        "@version": 1.1,
+        "Records": {
+          "@container": "@type",
+          "@id": "@graph"
+        },
+        "prov" : "http://www.w3.org/ns/prov#",
+        "xsd": "http://www.w3.org/2001/XMLSchema#",
+        "RRID": "http://scicrunch.org/resolver/",
+        "Id": "@id",
+        "Type": "@type",
+        "Label": "http://www.w3.org/2000/01/rdf-schema#label",
+        "StartedAtTime" : {
+          "@id": "prov:startedAtTime",
+          "@type": "http://www.w3.org/2001/XMLSchema#dateTime"
+        },
+        "EndedAtTime" : {
+          "@id": "prov:endedAtTime",
+          "@type": "xsd:dateTime"
+        },
+        "GeneratedBy" : {
+          "@id": "prov:wasGeneratedBy",
+          "@type": "@id"
+        },
+        "AttributedTo" : {
+          "@id": "prov:wasAttributedTo",
+          "@type": "@id"
+        },
+        "AssociatedWith" : {
+          "@id": "prov:wasAssociatedWith",
+          "@type": "@id"
+        },
+        "InformedBy" : {
+          "@id": "prov:wasInformedBy",
+          "@type": "@id"
+        },
+        "Used" : {
+          "@id": "prov:used",
+          "@type": "@id"
+        },
+        "ActedOnBehalfOf" : {
+          "@id": "prov:actedOnBehalfOf",
+          "@type": "@id"
+        },
+        "ProvEntities": "prov:Entity",
+        "Environments": "prov:Entity",
+        "Activities": "prov:Activity",
+        "Software": "prov:Agent",
+        "Atlocation": "prov:atLocation"
+    }
+}
diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml
index f5422abab2..4734941f22 100644
--- a/src/schema/objects/columns.yaml
+++ b/src/schema/objects/columns.yaml
@@ -146,6 +146,12 @@ description__entities:
   description: |
     Free-form text description of the entity's label (defined in `<entity>_id` column).
   type: string
+description__provenance:
+  name: description
+  display_name: Description
+  description: |
+    Free-form text description of the provenance file(s).
+  type: string
 dimension:
   name: dimension
   display_name: Dimension
@@ -388,6 +394,14 @@ plasma_radioactivity:
   description: |
     Radioactivity in plasma, in unit of plasma radioactivity (for example, `kBq/mL`).
   type: number
+provenance_label:
+  name: provenance_label
+  display_name: Provenance label
+  description: |
+    An identifier of the form `prov-<label>`,
+    matching a `prov` entity found in the dataset.
+  type: string
+  pattern: ^prov-[0-9a-zA-Z+]+$
 # reference column for channels.tsv files for EEG data
 reference__eeg:
   name: reference
diff --git a/src/schema/objects/datatypes.yaml b/src/schema/objects/datatypes.yaml
index 333cc4d922..cb16fa1b53 100644
--- a/src/schema/objects/datatypes.yaml
+++ b/src/schema/objects/datatypes.yaml
@@ -68,6 +68,11 @@ phenotype:
     Participant level measurement data
     (for example, responses from multiple questionnaires)
     split into individual files separate from `participants.tsv`.
+prov:
+  value: prov
+  display_name: Provenance
+  description: |
+    Provenance records describing how files in the dataset were generated.
 nirs:
   value: nirs
   display_name: Near-Infrared Spectroscopy
diff --git a/src/schema/objects/entities.yaml b/src/schema/objects/entities.yaml
index be94a5eb0a..7ecf4a4507 100644
--- a/src/schema/objects/entities.yaml
+++ b/src/schema/objects/entities.yaml
@@ -245,6 +245,13 @@ processing:
     exploited.
   type: string
   format: label
+prov:
+  name: prov
+  display_name: Provenance group
+  description: |
+    The `prov-<label>` entity allows to group related provenance files, using an arbitrary value for `<label>`.
+  type: string
+  format: label
 reconstruction:
   name: rec
   display_name: Reconstruction
diff --git a/src/schema/objects/files.yaml b/src/schema/objects/files.yaml
index 9c6bc41305..3339f07c9e 100644
--- a/src/schema/objects/files.yaml
+++ b/src/schema/objects/files.yaml
@@ -102,6 +102,13 @@ code:
     (for example the one used to generate the derivatives from the raw data).
     See the [Code section](SPEC_ROOT/modality-agnostic-files/code.md)
     for more information.
+prov:
+  display_name: Provenance
+  file_type: directory
+  description: |
+    A directory in which to store provenance metadata.
+    See the [Provenance section](SPEC_ROOT/modality-agnostic-files/provenance.md)
+    for more information.
 derivatives:
   display_name: Derivative data
   file_type: directory
diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index e6567a57f5..9169ce9746 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -48,6 +48,79 @@ AcquisitionVoxelSize:
     type: number
     exclusiveMinimum: 0
     unit: mm
+Activities:
+  name: Activities
+  display_name: Activities
+  description: Provenance objects describing activities.
+  type: array
+  minItems: 1
+  items:
+    type: object
+    required: [Id, Label, Command]
+    properties:
+      Id:
+        name: Id
+        description: "Identifier for the activity (see the [Consistency and uniqueness of identifiers]\
+        (SPEC_ROOT/modality-agnostic-files/provenance.md#consistency-and-uniqueness-of-identifiers) section)."
+        type: string
+        format: uri
+      Label:
+        name: Label
+        description: |
+          Name for the activity. This can be the name of the tool, script,
+          or function used (for example "bet", "recon-all", "myFunction.py", "docker").
+        type: string
+        format: label
+      Command:
+        name: Command
+        description: Command (or commands) used to run the tool, including all parameters.
+        type: string
+      AssociatedWith:
+        name: AssociatedWith
+        description: |
+          Identifier(s) of the software package(s) used to compute this activity.
+
+          Related software MUST be described as specified in the
+          [Software](SPEC_ROOT/modality-agnostic-files/provenance.md#software) section.
+        anyOf:
+          - type: string
+            format: uri
+          - type: array
+            items:
+              type: string
+              format: uri
+      Used:
+        name: Used
+        description: |
+          Identifier(s) of the provEntity (one or more) or environment (one or more) used by this activity.
+
+          Related provEntities MUST be described as specified in the
+          [ProvEntities](SPEC_ROOT/modality-agnostic-files/provenance.md#proventities) section.
+
+          Related environments MUST be described as specified in the
+          [Environments](SPEC_ROOT/modality-agnostic-files/provenance.md#environments) section.
+        anyOf:
+          - type: string
+            format: uri
+          - type: array
+            items:
+              type: string
+              format: uri
+      Type:
+        name: Type
+        description: A term from a controlled vocabulary that more specifically describes the activity.
+        type: string
+        format: uri
+      StartedAtTime:
+        name: StartedAtTime
+        description: A timestamp tracking when this activity started.
+        type: string
+        format: date
+      EndedAtTime:
+        name: EndedAtTime
+        description: A timestamp tracking when this activity ended.
+        type: string
+        format: date
 Anaesthesia:
   name: Anaesthesia
   display_name: Anaesthesia
@@ -776,7 +849,7 @@ Description__GeneratedBy:
   name: Description
   display_name: Pipeline Description
   description: |
-    Plain-text description of the pipeline or process that generated the outputs.
+    Plain-text description of the pipeline or process that generated the dataset.
     RECOMMENDED if `Name` is `"Manual"`.
   type: string
 DetectorType:
@@ -823,6 +896,17 @@ DewarPosition:
     `"upright"`, `"supine"` or `"degrees"` of angle from vertical:
     for example on CTF systems, `"upright=15°, supine=90°"`.
   type: string
+Digest:
+  name: Digest
+  display_name: Digest
+  description: |
+    Object containing digests of the data described by the provEntity.
+    Each key in the object MUST be the name of a checksum function if present in this list:
+    `MD5`; `SHA1`; `SHA-224` ; `SHA-256` ; `SHA-384` ; `SHA-512` ;
+    `SHA3-224`; `SHA3-256`; `SHA3-384`; `SHA3-512`; `BLAKE2B-256`; `BLAKE3-256`;
+    `SHAKE128`; `SHAKE256`. Otherwise, key MAY be an arbitrary label.
+    The corresponding value is the checksum as computed by the function.
+  type: object
 DigitizedHeadPoints:
   name: DigitizedHeadPoints
   display_name: Digitized Head Points
@@ -1176,6 +1260,104 @@ EncodingTechnique:
     For example, `"Cartesian"`, `"EPSI"`, `"Spiral"`,
     or `"Density-weighted concentric ring trajectory"`.
   type: string
+ProvEntities:
+  name: ProvEntities
+  display_name: ProvEntities
+  description: Provenance objects describing provEntities.
+  type: array
+  minItems: 1
+  items:
+    type: object
+    required: [Id, Label]
+    recommended: [Digest]
+    properties:
+      Id:
+        name: Id
+        description: "Identifier for the provEntity (see the [Consistency and uniqueness of identifiers]\
+        (SPEC_ROOT/modality-agnostic-files/provenance.md#consistency-and-uniqueness-of-identifiers) section)."
+        type: string
+        format: uri
+      Label:
+        name: Label
+        description: A name for the provEntity.
+        type: string
+        format: label
+      Digest:
+        name: Digest
+        description: |
+          Object containing digests of the data described by the provEntity.
+          Each key in the object MUST be the name of a checksum function if present in this list:
+          `MD5`; `SHA1`; `SHA-224` ; `SHA-256` ; `SHA-384` ; `SHA-512` ;
+          `SHA3-224`; `SHA3-256`; `SHA3-384`; `SHA3-512`; `BLAKE2B-256`; `BLAKE3-256`;
+          `SHAKE128`; `SHAKE256`. Otherwise, key MAY be an arbitrary label.
+          The corresponding value is the checksum as computed by the function.
+        type: object
+      AtLocation:
+        name: AtLocation
+        description: |
+          For input files, this is the relative path to the file on disk.
+        type: string
+      GeneratedBy:
+        name: GeneratedBy
+        description: |
+          Identifier(s) of the activity (one or more) responsible for the creation of the provEntity.
+
+          Related activities MUST be described as specified in the
+          [Activities](SPEC_ROOT/modality-agnostic-files/provenance.md#activities) section.
+        anyOf:
+          - type: string
+            format: uri
+          - type: array
+            minItems: 1
+            items:
+              type: string
+              format: uri
+      Type:
+        name: Type
+        description: A term from a controlled vocabulary that more specifically describes the provEntity.
+        type: string
+        format: uri
+ProvEntityType:
+  name: Type
+  display_name: Type
+  description: |
+    A term from a controlled vocabulary that more specifically describes a ProvEntity.
+  type: string
+  format: uri
+Environments:
+  name: Environments
+  display_name: Environments
+  description: Provenance objects describing environments.
+  type: array
+  minItems: 1
+  items:
+    type: object
+    required: [Id, Label]
+    properties:
+      Id:
+        name: Id
+        description: "Identifier for the environment (see the [Consistency and uniqueness of identifiers]\
+        (SPEC_ROOT/modality-agnostic-files/provenance.md#consistency-and-uniqueness-of-identifiers) section)."
+        type: string
+        format: uri
+      Label:
+        name: Label
+        description: A name for the environment.
+        type: string
+        format: label
+      EnvVars:
+        name: EnvVars
+        description: A dictionary defining the environment variables as key-value pairs.
+        type: object
+      OperatingSystem:
+        name: OperatingSystem
+        description: Name of the operating system.
+        type: string
+      Dependencies:
+        name: Dependencies
+        description: |
+          A dictionary defining the software used as dependencies and their versions as key-value pairs.
+        type: object
 EpochLength:
   name: EpochLength
   display_name: Epoch Length
@@ -1377,8 +1559,7 @@ Funding:
 GeneratedBy:
   name: GeneratedBy
   display_name: Generated By
-  description: |
-    Used to specify provenance of the dataset.
+  description: Used to specify provenance of the dataset.
   type: array
   minItems: 1
   items:
@@ -1396,6 +1577,22 @@ GeneratedBy:
         $ref: objects.metadata.CodeURL
       Container:
         $ref: objects.metadata.Container
+GeneratedById:
+  name: GeneratedBy
+  display_name: Generated By
+  description: |
+    Identifier(s) of the activity (one or more) responsible for the creation of the provEntity.
+
+    Related activities MUST be described as specified in the
+    [Activities](SPEC_ROOT/modality-agnostic-files/provenance.md#activities) section.
+  anyOf:
+    - type: string
+      format: uri
+    - type: array
+      minItems: 1
+      items:
+        type: string
+        format: uri
 GeneticLevel:
   name: GeneticLevel
   display_name: Genetic Level
@@ -2367,7 +2564,7 @@ Name__GeneratedBy:
   name: Name
   display_name: Pipeline Name
   description: |
-    Name of the pipeline or process that generated the outputs. Use `"Manual"` to
+    Name of the pipeline or process that generated the dataset. Use `"Manual"` to
     indicate the derivatives were generated by hand, or adjusted manually after an
     initial run of an automated pipeline.
   type: string
@@ -3424,6 +3621,22 @@ ShortChannelCount:
     The number of short channels. 0 indicates no short channels.
   type: integer
   minimum: 0
+SidecarGeneratedBy:
+  name: SidecarGeneratedBy
+  display_name: Sidecar Generated By
+  description: |
+    Identifier(s) of the activity (one or more) responsible for the creation of the sidecar JSON file.
+
+    Related activities MUST be described as specified in the
+    [Activities](SPEC_ROOT/modality-agnostic-files/provenance.md#activities) section.
+  anyOf:
+    - type: string
+      format: uri
+    - type: array
+      minItems: 1
+      items:
+        type: string
+        format: uri
 SinglesRate:
   name: SinglesRate
   display_name: Singles Rate
@@ -3492,6 +3705,48 @@ SliceTiming:
     type: number
     minimum: 0
     unit: s
+Software:
+  name: Software
+  display_name: Software
+  description: Provenance objects describing software.
+  type: array
+  minItems: 1
+  items:
+    type: object
+    required: [Id, Label, Version]
+    properties:
+      Id:
+        name: Id
+        description: "Identifier for the software package (see the [Consistency and uniqueness of identifiers]\
+        (SPEC_ROOT/modality-agnostic-files/provenance.md#consistency-and-uniqueness-of-identifiers) section)."
+        type: string
+        format: uri
+      Label:
+        name: Label
+        description: Name of the software package.
+        type: string
+        format: label
+      Version:
+        name: Version
+        description: Version of the software package.
+        type: string
+      AltIdentifier:
+        name: AltIdentifier
+        description: URI of the RRID for this software package (cf. https://rrid.site/).
+        type: string
+        format: uri
+      ActedOnBehalfOf:
+        name: ActedOnBehalfOf
+        description: |
+          Identifier of another software package that was responsible for using this software package
+          in the context of the activities associated to it.
+
+          Example: if software A launches software B to perform activity C, then B ActedOnBehalfOf A.
+
+          Related software MUST be described as specified in the
+          [Software](SPEC_ROOT/modality-agnostic-files/provenance.md#software) section.
+        type: string
+        format: uri
 SoftwareFilters:
   name: SoftwareFilters
   display_name: Software Filters
@@ -4021,7 +4276,7 @@ Version__Dataset:
 Version__GeneratedBy:
   name: Version
   display_name: Pipeline Version
-  description: Version of the pipeline
+  description: Version of the pipeline or process that generated the dataset.
   type: string
 VolumeAffineMatrix:
   name: VolumeAffineMatrix
diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml
index 1e2825ced2..475d8d5011 100644
--- a/src/schema/objects/suffixes.yaml
+++ b/src/schema/objects/suffixes.yaml
@@ -502,6 +502,12 @@ VFA:
     Depending on the provided metadata fields and the sequence type,
     data may be eligible for DESPOT1, DESPOT2 and their variants
     ([Deoni et al. 2005](https://doi.org/10.1002/mrm.20314)).
+act:
+  value: act
+  display_name: Activities
+  description: |
+    A JSON file containing provenance objects describing activities.
+    (See the [`Activities`](SPEC_ROOT/modality-agnostic-files/provenance.md#activities) section).
 angio:
   value: angio
   display_name: Angiogram
@@ -612,6 +618,18 @@ electrodes:
   display_name: Electrodes
   description: |
     File that gives the location of (i)EEG electrodes.
+ent:
+  value: ent
+  display_name: ProvEntities
+  description: |
+    A JSON file containing provenance objects describing provEntities.
+    (See the [`ProvEntities`](SPEC_ROOT/modality-agnostic-files/provenance.md#proventities) section).
+env:
+  value: env
+  display_name: Environments
+  description: |
+    A JSON file containing provenance objects describing environments.
+    (See the [`Environments`](SPEC_ROOT/modality-agnostic-files/provenance.md#environments) section).
 epi:
   value: epi
   display_name: EPI
@@ -817,6 +835,12 @@ probseg:
     A probabilistic segmentation.
 
     This suffix may only be used in derivative datasets.
+soft:
+  value: soft
+  display_name: Software
+  description: |
+    A JSON file containing provenance objects describing software.
+    (See the [`Software`](SPEC_ROOT/modality-agnostic-files/provenance.md#software) section).
 sbref:
   value: sbref
   display_name: Single-band reference image
diff --git a/src/schema/rules/dataset_metadata.yaml b/src/schema/rules/dataset_metadata.yaml
index b9c8e74761..9e7a66088d 100644
--- a/src/schema/rules/dataset_metadata.yaml
+++ b/src/schema/rules/dataset_metadata.yaml
@@ -17,7 +17,8 @@ dataset_description:
     EthicsApprovals: optional
     ReferencesAndLinks: optional
     DatasetDOI: optional
-    GeneratedBy: recommended
+    GeneratedBy: recommended if `GeneratedById` is not present
+    GeneratedById: recommended if `GeneratedById` is not present
     SourceDatasets: recommended
 
 dataset_authors:
@@ -39,7 +40,8 @@ derivative_description:
     - path == "/dataset_description.json"
     - json.DatasetType == "derivative"
   fields:
-    GeneratedBy: required
+    GeneratedBy: required if `GeneratedById` is not present
+    GeneratedById: required if `GeneratedBy` is not present
 
 dataset_description_with_genetics:
   selectors:
diff --git a/src/schema/rules/directories.yaml b/src/schema/rules/directories.yaml
index e5415e8c14..bdbf99a643 100644
--- a/src/schema/rules/directories.yaml
+++ b/src/schema/rules/directories.yaml
@@ -23,6 +23,7 @@ study:
       - docs
       - derivatives
       - logs
+      - prov
       - sourcedata
   code:
     name: code
@@ -40,6 +41,10 @@ study:
     name: logs
     level: optional
     opaque: true
+  prov:
+    name: prov
+    level: optional
+    opaque: false
   sourcedata:
     name: sourcedata
     level: optional
@@ -53,6 +58,7 @@ raw:
       - derivatives
       - logs
       - phenotype
+      - prov
       - sourcedata
       - stimuli
       - subject
@@ -76,6 +82,10 @@ raw:
     name: phenotype
     level: optional
     opaque: false
+  prov:
+    name: prov
+    level: optional
+    opaque: false
   sourcedata:
     name: sourcedata
     level: optional
@@ -111,6 +121,7 @@ derivative:
       - derivatives
       - logs
       - phenotype
+      - prov
       - sourcedata
       - stimuli
       - subject
@@ -134,6 +145,10 @@ derivative:
     name: phenotype
     level: optional
     opaque: false
+  prov:
+    name: prov
+    level: optional
+    opaque: false
   sourcedata:
     name: sourcedata
     level: optional
diff --git a/src/schema/rules/entities.yaml b/src/schema/rules/entities.yaml
index 44174d333e..2cebaf977e 100644
--- a/src/schema/rules/entities.yaml
+++ b/src/schema/rules/entities.yaml
@@ -31,4 +31,5 @@
 - resolution
 - density
 - label
+- prov
 - description
diff --git a/src/schema/rules/files/common/core.yaml b/src/schema/rules/files/common/core.yaml
index fe8535d0ce..d83b7cd580 100644
--- a/src/schema/rules/files/common/core.yaml
+++ b/src/schema/rules/files/common/core.yaml
@@ -36,6 +36,9 @@ code:
 derivatives:
   level: optional
   path: derivatives
+prov:
+  level: optional
+  path: prov
 docs:
   level: optional
   path: docs
diff --git a/src/schema/rules/files/common/modality_agnostic.yaml b/src/schema/rules/files/common/modality_agnostic.yaml
new file mode 100644
index 0000000000..146b98f4a3
--- /dev/null
+++ b/src/schema/rules/files/common/modality_agnostic.yaml
@@ -0,0 +1,18 @@
+---
+# Files and directories that can be found at any level of a dataset.
+
+# Provenance json files
+provenance:
+  level: optional
+  datatypes:
+    - prov
+  suffixes:
+    - act
+    - ent
+    - env
+    - soft
+  extensions:
+    - .json
+  entities:
+    prov: required
+    description: optional
diff --git a/src/schema/rules/files/common/tables.yaml b/src/schema/rules/files/common/tables.yaml
index 21f03f6579..155bed0084 100644
--- a/src/schema/rules/files/common/tables.yaml
+++ b/src/schema/rules/files/common/tables.yaml
@@ -5,6 +5,12 @@ participants:
   extensions:
     - .tsv
     - .json
+provenance:
+  level: optional
+  stem: provenance
+  extensions:
+    - .tsv
+    - .json
 samples:
   level: optional
   stem: samples
diff --git a/src/schema/rules/json/prov.yaml b/src/schema/rules/json/prov.yaml
new file mode 100644
index 0000000000..90102bfdf6
--- /dev/null
+++ b/src/schema/rules/json/prov.yaml
@@ -0,0 +1,28 @@
+---
+ActivitiesProvenanceFile:
+  selectors:
+    - datatype == "prov"
+    - suffix == "act"
+  fields:
+    Activities: required
+
+EnvironmentsProvenanceFile:
+  selectors:
+    - datatype == "prov"
+    - suffix == "env"
+  fields:
+    Environments: required
+
+ProvEntitiesProvenanceFile:
+  selectors:
+    - datatype == "prov"
+    - suffix == "ent"
+  fields:
+    ProvEntities: required
+
+SoftwareProvenanceFile:
+  selectors:
+    - datatype == "prov"
+    - suffix == "soft"
+  fields:
+    Software: required
diff --git a/src/schema/rules/tabular_data/modality_agnostic.yaml b/src/schema/rules/tabular_data/modality_agnostic.yaml
index 83fd7e14f4..cf402e538e 100644
--- a/src/schema/rules/tabular_data/modality_agnostic.yaml
+++ b/src/schema/rules/tabular_data/modality_agnostic.yaml
@@ -74,3 +74,16 @@ Phenotype:
     HED: optional
   index_columns: [participant_id]
   additional_columns: allowed
+
+Provenance:
+  selectors:
+    - datatype == 'prov'
+    - stem == 'provenance'
+    - extension == '.tsv'
+  initial_columns:
+    - provenance_label
+  columns:
+    provenance_label: required
+    description__provenance: optional
+  index_columns: [provenance_label]
+  additional_columns: allowed
diff --git a/tools/schemacode/src/bidsschematools/render/text.py b/tools/schemacode/src/bidsschematools/render/text.py
index dd97e5c926..18f745e7ba 100644
--- a/tools/schemacode/src/bidsschematools/render/text.py
+++ b/tools/schemacode/src/bidsschematools/render/text.py
@@ -244,9 +244,9 @@ def make_filename_template(
 
     Parameters
     ----------
-    dstype : "raw" or "deriv"
-        The type of files being rendered; determines if rules are found in rules.files.raw
-        or rules.files.deriv
+    dstype : "raw", "deriv" or "common"
+        The type of files being rendered; determines if rules are found in rules.files.raw,
+        rules.files.deriv or rules.files.common
     schema : dict
         The schema object, which is a dictionary with nested dictionaries and
         lists stored within it.
@@ -307,25 +307,31 @@ def make_filename_template(
     ext_key_table = value_key_table(schema.objects.extensions)
 
     # Parent directories
-    sub_string = utils._link_with_html(
-        _format_entity(schema.objects.entities.subject, lt, gt),
-        html_path=ENTITIES_PATH + ".html",
-        heading="sub",
-        pdf_format=pdf_format,
-    )
-    ses_string = utils._link_with_html(
-        _format_entity(schema.objects.entities.session, lt, gt),
-        html_path=ENTITIES_PATH + ".html",
-        heading="ses",
-        pdf_format=pdf_format,
-    )
-    lines = [f"{sub_string}/", f"\t[{ses_string}/]"]
+    if dstype != "common":
+        sub_string = utils._link_with_html(
+            _format_entity(schema.objects.entities.subject, lt, gt),
+            html_path=ENTITIES_PATH + ".html",
+            heading="sub",
+            pdf_format=pdf_format,
+        )
+        ses_string = utils._link_with_html(
+            _format_entity(schema.objects.entities.session, lt, gt),
+            html_path=ENTITIES_PATH + ".html",
+            heading="ses",
+            pdf_format=pdf_format,
+        )
+        lines = [f"{sub_string}/", f"\t[{ses_string}/]"]
+        datatype_indent = "\t\t"
+    else:
+        lines = []
+        datatype_indent = ""
 
     file_rules = schema.rules.files[dstype]
     file_groups = {}
     for rule in file_rules.values(level=2):
-        for datatype in rule.datatypes:
-            file_groups.setdefault(datatype, []).append(rule)
+        if "datatypes" in rule:
+            for datatype in rule.datatypes:
+                file_groups.setdefault(datatype, []).append(rule)
 
     if empty_dirs is None:
         empty_dirs = not placeholders
@@ -354,7 +360,7 @@ def make_filename_template(
             heading=f"{datatype.lower()}-datatypes",
             pdf_format=pdf_format,
         )
-        group_lines.append(f"\t\t{datatype_string}/")
+        group_lines.append(f"{datatype_indent}{datatype_string}/")
 
         # Unique filename patterns
         for group in file_groups[datatype]:
@@ -448,7 +454,7 @@ def make_filename_template(
             )
 
             group_lines.extend(
-                f"\t\t\t{ent_string}_{suffix}{extension}"
+                f"\t{datatype_indent}{ent_string}_{suffix}{extension}"
                 for suffix in sorted(suffixes)
                 for extension in sorted(extensions)
             )