diff --git a/Framework/PythonInterface/plugins/algorithms/IntegratePeaksSkew.py b/Framework/PythonInterface/plugins/algorithms/IntegratePeaksSkew.py
index 48bdc5c4242b..4a6adfeaa0d4 100644
--- a/Framework/PythonInterface/plugins/algorithms/IntegratePeaksSkew.py
+++ b/Framework/PythonInterface/plugins/algorithms/IntegratePeaksSkew.py
@@ -651,16 +651,16 @@ def plot_integrated_peak(self, fig, ax, ipk, norm_func):
             xmask, ymask = np.where(self.peak_mask.T)
             ax[0].lines[0].set_xdata(xmask)
             ax[0].lines[0].set_ydata(ymask)
-            ax[0].lines[1].set_xdata(self.icol)
-            ax[0].lines[1].set_ydata(self.irow)
+            ax[0].lines[1].set_xdata([self.icol])
+            ax[0].lines[1].set_ydata([self.irow])
             img.set_extent([-0.5, self.x_integrated_data.shape[1] - 0.5, self.x_integrated_data.shape[0] - 0.5, -0.5])
             # update 1D focused spectrum
             # vlines
             xmin_line, xmax_line, data, xpos_line, xmin_init_line, xmax_init_line, y0 = ax[1].lines
-            xmin_line.set_xdata(self.xmin_opt)
-            xmax_line.set_xdata(self.xmax_opt)
-            xmin_init_line.set_xdata(self.xmin)
-            xmax_init_line.set_xdata(self.xmax)
+            xmin_line.set_xdata([self.xmin_opt])
+            xmax_line.set_xdata([self.xmax_opt])
+            xmin_init_line.set_xdata([self.xmin])
+            xmax_init_line.set_xdata([self.xmax])
             xpos_line.set_xdata([self.xpos])
             # spectrum
             yerr = np.sqrt(self.epk_sq[istart:iend])
diff --git a/conda/recipes/conda_build_config.yaml b/conda/recipes/conda_build_config.yaml
index 567c22f601bc..49ddc8254b99 100644
--- a/conda/recipes/conda_build_config.yaml
+++ b/conda/recipes/conda_build_config.yaml
@@ -66,7 +66,7 @@ numpy:
   - 2.0.*
 
 matplotlib:
-  - 3.8.*
+  - 3.9.*
 
 mslice:
   - '2.10'
diff --git a/docs/source/release/v6.12.0/Framework/Dependencies/New_features/38077.rst b/docs/source/release/v6.12.0/Framework/Dependencies/New_features/38077.rst
index 0e63b094dbab..1216a6c2376d 100644
--- a/docs/source/release/v6.12.0/Framework/Dependencies/New_features/38077.rst
+++ b/docs/source/release/v6.12.0/Framework/Dependencies/New_features/38077.rst
@@ -1 +1 @@
-- Updated Matplotlib from version 3.7 to version 3.8. The release notes for version 3.8 can be found `here <https://matplotlib.org/stable/users/prev_whats_new/whats_new_3.8.0.html>`_ .
+- Updated Matplotlib from version 3.7 to version 3.9. The release notes for `version 3.8 <https://matplotlib.org/stable/users/prev_whats_new/whats_new_3.8.0.html>`_  and `version 3.9 <https://matplotlib.org/stable/users/prev_whats_new/whats_new_3.9.0.html>`_
diff --git a/qt/python/mantidqt/mantidqt/plotting/test/test_sample_shape.py b/qt/python/mantidqt/mantidqt/plotting/test/test_sample_shape.py
index 20e735d4469c..7c37722b8604 100644
--- a/qt/python/mantidqt/mantidqt/plotting/test/test_sample_shape.py
+++ b/qt/python/mantidqt/mantidqt/plotting/test/test_sample_shape.py
@@ -8,7 +8,7 @@
 #
 #
 
-from numpy.testing import assert_array_equal, assert_allclose, assert_almost_equal
+from numpy.testing import assert_array_equal, assert_allclose, assert_array_less
 from os import path, remove
 from tempfile import gettempdir
 from unittest import TestCase, main
@@ -268,7 +268,7 @@ def test_set_axes_to_largest_mesh(self, mock_call_overall_limits_for_all_meshes)
         xlim = axes.get_xlim()
         ylim = axes.get_ylim()
         zlim = axes.get_zlim()
-        assert_almost_equal(xlim, (-0.165, 0.165), 5)  # extra 5%
+        assert_array_less((0.15, 0.15), np.abs(xlim))  # window is bigger than object 15cm
         assert_allclose(xlim, ylim, rtol=self.RELATIVE_TOLERANCE)
         assert_allclose(xlim, zlim, rtol=self.RELATIVE_TOLERANCE)
 
diff --git a/qt/python/mantidqt/mantidqt/widgets/plotconfigdialog/__init__.py b/qt/python/mantidqt/mantidqt/widgets/plotconfigdialog/__init__.py
index 387d6bb9294d..1108f02bb03c 100644
--- a/qt/python/mantidqt/mantidqt/widgets/plotconfigdialog/__init__.py
+++ b/qt/python/mantidqt/mantidqt/widgets/plotconfigdialog/__init__.py
@@ -7,7 +7,7 @@
 #  This file is part of the mantid workbench.
 
 from mantid.plots.utility import row_num, col_num
-from matplotlib.axes import ErrorbarContainer
+from matplotlib.container import ErrorbarContainer
 from matplotlib.collections import QuadMesh
 from mpl_toolkits.mplot3d.art3d import Poly3DCollection
 
diff --git a/qt/python/mantidqt/mantidqt/widgets/plotconfigdialog/curvestabwidget/__init__.py b/qt/python/mantidqt/mantidqt/widgets/plotconfigdialog/curvestabwidget/__init__.py
index fe50bf9959e4..6a03cc822d72 100644
--- a/qt/python/mantidqt/mantidqt/widgets/plotconfigdialog/curvestabwidget/__init__.py
+++ b/qt/python/mantidqt/mantidqt/widgets/plotconfigdialog/curvestabwidget/__init__.py
@@ -7,7 +7,7 @@
 #  This file is part of the mantid workbench.
 
 from matplotlib import rcParams
-from matplotlib.axes import ErrorbarContainer
+from matplotlib.container import ErrorbarContainer
 from matplotlib.lines import Line2D
 from numpy import isclose
 from qtpy.QtCore import Qt