diff --git a/docs/guides/transactions.md b/docs/guides/transactions.md
index 4676e1e7..2cc67e1b 100644
--- a/docs/guides/transactions.md
+++ b/docs/guides/transactions.md
@@ -20,9 +20,9 @@ from lakefs_spec import LakeFSFileSystem
 fs = LakeFSFileSystem()
 
 with fs.transaction("repo", "main") as tx:
-    fs.put_file("train-data.txt", f"repo/{tx.branch.id}/train-data.txt")
+    fs.put_file("train-data.txt", "train-data.txt")
     tx.commit(message="Add training data")
-    fs.put_file("test-data.txt", f"repo/{tx.branch.id}/test-data.txt")
+    fs.put_file("test-data.txt", "test-data.txt")
     sha = tx.commit(message="Add test data")
     tx.tag(sha, name="My train-test split")
 ```
@@ -35,6 +35,13 @@ The full list of supported lakeFS versioning operations (by default, these opera
 * [`rev_parse`](../reference/lakefs_spec/transaction.md#lakefs_spec.transaction.LakeFSTransaction.rev_parse), for parsing revisions like branch/tag names and SHA fragments into full commit SHAs.
 * [`tag`](../reference/lakefs_spec/transaction.md#lakefs_spec.transaction.LakeFSTransaction.tag), for creating a tag pointing to a commit.
 
+## Limitations of transactions
+
+Transactions are scoped to a single repository and branch only, equal to those given to the `fs.transaction()` context manager.
+When uploading files in a transaction via `fs.put()` or `fs.put_file()`, you **must** give all remote paths as file names.
+If you use a fully qualified URI, leading repository and branch names will be interpreted as subdirectories, which will be created on upload.
+No warnings or errors will be thrown, so be sure to double-check your paths in all transaction scopes.
+
 ## Lifecycle of ephemeral transaction branches
 
 You can control the lifecycle for a transaction branch with the `delete` argument:
@@ -56,7 +63,7 @@ from lakefs_spec import LakeFSFileSystem
 fs = LakeFSFileSystem()
 
 with fs.transaction("repo", "main", delete="onsuccess") as tx:
-    fs.put_file("my-file.txt", f"repo/{tx.branch.id}/my-file.txt")
+    fs.put_file("my-file.txt", "my-file.txt")
     tx.commit(message="Add my-file.txt")
     raise ValueError("oops!")
 ```
diff --git a/src/lakefs_spec/spec.py b/src/lakefs_spec/spec.py
index 18666c22..8669d595 100644
--- a/src/lakefs_spec/spec.py
+++ b/src/lakefs_spec/spec.py
@@ -170,6 +170,20 @@ def wrapped_api_call(
         except ServerException as e:
             raise translate_lakefs_error(e, rpath=rpath, message=message, set_cause=set_cause)
 
+    def make_uri(self, path: str | os.PathLike[str]) -> str:
+        spath = stringify_path(path)
+        # NB: this fails silently if the input path is already fully qualified.
+        # However, in general, it's impossible to distinguish between a
+        # fully qualified path and a normal nested path, so at most, we
+        # could split off the first segment of the input and check it against existing
+        # repositories.
+        if self._intrans:
+            prefix = "/".join([self.transaction.repository, self.transaction.branch.id])
+            if spath.startswith(prefix):
+                return spath
+            return prefix + "/" + spath
+        return spath
+
     def checksum(self, path: str | os.PathLike[str]) -> str | None:
         """
         Get a remote lakeFS file object's checksum.
@@ -186,7 +200,7 @@ def checksum(self, path: str | os.PathLike[str]) -> str | None:
         str | None
             The remote file's checksum, or ``None`` if ``path`` points to a directory or does not exist.
         """
-        path = stringify_path(path)
+        path = self.make_uri(path)
         try:
             return self.info(path).get("checksum")
         except FileNotFoundError:
@@ -218,7 +232,7 @@ def exists(self, path: str | os.PathLike[str], **kwargs: Any) -> bool:
         PermissionError
             If the user does not have sufficient permissions to query object existence.
         """
-        path = stringify_path(path)
+        path = self.make_uri(path)
         repository, ref, resource = parse(path)
         try:
             reference = lakefs.Reference(repository, ref, client=self.client)
@@ -261,8 +275,8 @@ def cp_file(
         ValueError
             When attempting to copy objects between repositories.
         """
-        path1 = stringify_path(path1)
-        path2 = stringify_path(path2)
+        path1 = self.make_uri(path1)
+        path2 = self.make_uri(path2)
         if path1 == path2:
             return
 
@@ -306,7 +320,7 @@ def get_file(
         **kwargs: Any
             Additional keyword arguments passed to ``AbstractFileSystem.open()``.
         """
-        rpath = stringify_path(rpath)
+        rpath = self.make_uri(rpath)
         lpath = stringify_path(lpath)
 
         if precheck and Path(lpath).is_file():
@@ -343,7 +357,7 @@ def info(self, path: str | os.PathLike[str], **kwargs: Any) -> dict[str, Any]:
         FileNotFoundError
             If the ``path`` refers to a non-file path that does not exist in the repository.
         """
-        path = stringify_path(path)
+        path = self.make_uri(path)
         repository, ref, resource = parse(path)
         # first, try with `stat_object` in case of a file.
         # the condition below checks edge cases of resources that cannot be files.
@@ -481,6 +495,7 @@ def ls(
             A list of all objects' metadata under the given remote path if ``detail=True``, or alternatively only their names if ``detail=False``.
         """
         path = self._strip_protocol(path)
+        path = self.make_uri(path)
         repository, ref, prefix = parse(path)
 
         recursive = kwargs.pop("recursive", False)
@@ -557,6 +572,7 @@ def ls(
             # To make recursive ls behave identical to the non-recursive case,
             # add back virtual `directory` entries, which are only returned by
             # the lakeFS API when querying non-recursively.
+            # TODO: Fix this up for intrans
             here = self._strip_protocol(path).rstrip("/")
             subdirs = {parent for o in info if (parent := self._parent(o["name"])) != here}
             for subdir in subdirs:
@@ -623,7 +639,7 @@ def open(
         if mode not in {"r", "rb", "w", "wb", "x", "xb"}:
             raise NotImplementedError(f"unsupported mode {mode!r}")
 
-        path = stringify_path(path)
+        path = self.make_uri(path)
         repo, ref, resource = parse(path)
 
         if mode.startswith("r"):
@@ -682,7 +698,7 @@ def put_file(
             Additional keyword arguments to pass to ``LakeFSFileSystem.open()``.
         """
         lpath = stringify_path(lpath)
-        rpath = stringify_path(rpath)
+        rpath = self.make_uri(rpath)
 
         if precheck and Path(lpath).is_file():
             remote_checksum = self.checksum(rpath)
@@ -730,7 +746,7 @@ def rm(
             possible.
         """
 
-        path = stringify_path(path)
+        path = self.make_uri(path)
         repository, ref, prefix = parse(path)
 
         with self.wrapped_api_call(rpath=path):
diff --git a/tests/test_put_file.py b/tests/test_put_file.py
index 9c85ddf3..1f6249ec 100644
--- a/tests/test_put_file.py
+++ b/tests/test_put_file.py
@@ -21,7 +21,7 @@ def test_no_change_postcommit(
     message = f"Add file {random_file.name}"
 
     with fs.transaction(repository, temp_branch) as tx:
-        fs.put(lpath, f"{repository.id}/{tx.branch.id}/{random_file.name}")
+        fs.put(lpath, random_file.name)
         tx.commit(message=message)
 
     commits = list(temp_branch.log(max_amount=2))
@@ -31,8 +31,8 @@ def test_no_change_postcommit(
 
     # put the same file again, this time the diff is empty
     with fs.transaction(repository, temp_branch) as tx:
-        fs.put(lpath, f"{repository.id}/{tx.branch.id}/{random_file.name}", precheck=False)
-        tx.commit(message=f"Add file {random_file.name}")
+        fs.put(lpath, random_file.name, precheck=False)
+        tx.commit(message=message)
 
     # check that no other commit has happened.
     assert temp_branch.head.get_commit() == current_head
diff --git a/tests/test_rm.py b/tests/test_rm.py
index 8026ff91..8e98c017 100644
--- a/tests/test_rm.py
+++ b/tests/test_rm.py
@@ -28,7 +28,7 @@ def test_rm_with_transaction(
     message = "Remove file README.md"
 
     with fs.transaction(repository, temp_branch, automerge=True) as tx:
-        fs.rm(f"{repository.id}/{tx.branch.id}/README.md")
+        fs.rm("README.md")
         tx.commit(message=message)
 
     commits = list(temp_branch.log(max_amount=2))
diff --git a/tests/test_transactions.py b/tests/test_transactions.py
index 032c61a2..61fb1ebb 100644
--- a/tests/test_transactions.py
+++ b/tests/test_transactions.py
@@ -17,12 +17,11 @@ def test_transaction_commit(
     random_file = random_file_factory.make()
 
     lpath = str(random_file)
-    rpath = f"{repository.id}/{temp_branch.id}/{random_file.name}"
 
     message = f"Add file {random_file.name}"
 
     with fs.transaction(repository, temp_branch) as tx:
-        fs.put_file(lpath, f"{repository.id}/{tx.branch.id}/{random_file.name}")
+        fs.put_file(lpath, random_file.name)
         assert len(tx.files) == 1
         # sha is a placeholder for the actual SHA created on transaction completion.
         sha = tx.commit(message=message)
@@ -65,7 +64,7 @@ def test_transaction_merge(
             tbname = tx.branch.id
             lpath = str(random_file)
             # stage a file on the transaction branch...
-            fs.put_file(lpath, f"{repository.id}/{tx.branch.id}/{random_file.name}")
+            fs.put_file(lpath, random_file.name)
             # ... commit it with the above message
             tx.commit(message=message)
             # ... and merge it into temp_branch.
@@ -90,7 +89,7 @@ def test_transaction_revert(
     message = f"Add file {random_file.name}"
 
     with fs.transaction(repository, temp_branch, automerge=True) as tx:
-        fs.put_file(lpath, f"{repository.id}/{tx.branch.id}/{random_file.name}")
+        fs.put_file(lpath, random_file.name)
         tx.commit(message=message)
         revert_commit = tx.revert(temp_branch, temp_branch.head)
 
@@ -113,7 +112,7 @@ def test_transaction_failure(
 
     try:
         with fs.transaction(repository, temp_branch) as tx:
-            fs.put_file(lpath, f"{repository.id}/{tx.branch.id}/{random_file.name}")
+            fs.put_file(lpath, random_file.name)
             tx.commit(message=message)
             raise RuntimeError("something went wrong")
     except RuntimeError:
@@ -159,8 +158,8 @@ def test_warn_uncommitted_changes(
     lpath = str(random_file)
 
     with pytest.warns(match="uncommitted changes.*lost"):
-        with fs.transaction(repository, temp_branch) as tx:
-            fs.put_file(lpath, f"{repository.id}/{tx.branch.id}/{random_file.name}")
+        with fs.transaction(repository, temp_branch):
+            fs.put_file(lpath, random_file.name)
 
 
 def test_warn_uncommitted_changes_on_persisted_branch(
@@ -175,4 +174,4 @@ def test_warn_uncommitted_changes_on_persisted_branch(
 
     with pytest.warns(match="uncommitted changes(?:(?!lost).)*$"):
         with fs.transaction(repository, temp_branch, delete="never") as tx:
-            fs.put_file(lpath, f"{repository.id}/{tx.branch.id}/{random_file.name}")
+            fs.put_file(lpath, random_file.name)