diff --git a/scripts/addons_core/io_scene_fbx/__init__.py b/scripts/addons_core/io_scene_fbx/__init__.py
index 8f195a4175d..bb36400aa91 100644
--- a/scripts/addons_core/io_scene_fbx/__init__.py
+++ b/scripts/addons_core/io_scene_fbx/__init__.py
@@ -5,7 +5,7 @@
 bl_info = {
     "name": "FBX format",
     "author": "Campbell Barton, Bastien Montagne, Jens Restemeier, @Mysteryem",
-    "version": (5, 12, 5),
+    "version": (5, 12, 6),
     "blender": (4, 2, 0),
     "location": "File > Import-Export",
     "description": "FBX IO meshes, UVs, vertex colors, materials, textures, cameras, lamps and actions",
diff --git a/scripts/addons_core/io_scene_fbx/export_fbx_bin.py b/scripts/addons_core/io_scene_fbx/export_fbx_bin.py
index 04749b199f3..cfa8c371f46 100644
--- a/scripts/addons_core/io_scene_fbx/export_fbx_bin.py
+++ b/scripts/addons_core/io_scene_fbx/export_fbx_bin.py
@@ -2681,17 +2681,23 @@ def fbx_data_from_scene(scene, depsgraph, settings):
             # NOTE: The dependency graph might be re-evaluating multiple times, which could
             # potentially free the mesh created early on. So we put those meshes to bmain and
             # free them afterwards. Not ideal but ensures correct ownership.
+            # This also converts non-mesh Objects to Mesh data.
             tmp_me = bpy.data.meshes.new_from_object(
                 ob_to_convert, preserve_all_data_layers=True, depsgraph=depsgraph)
 
-            # Usually the materials of the evaluated object will be the same, but modifiers, such as Geometry Nodes,
-            # can change the materials.
-            orig_mats = tuple(slot.material for slot in ob.material_slots)
-            eval_mats = tuple(slot.material.original if slot.material else None
-                              for slot in ob_to_convert.material_slots)
+            # Usually the materials of the evaluated Object converted to a Mesh will be the same as the original
+            # Object, but modifiers, such as Geometry Nodes, can change the materials.
+            orig_mats = [slot.material for slot in ob.material_slots]
+            eval_mats = list(tmp_me.materials)
             if orig_mats != eval_mats:
+                # An object-linked material slot replaces the material on the data at the slot's index. If applying
+                # modifiers changes the materials on the data, the object-linked material slot will replace the new
+                # material at the same index as before.
+                for i, slot in zip(range(len(eval_mats)), ob.material_slots):
+                    if slot.link == 'OBJECT':
+                        eval_mats[i] = slot.material
                 # Override the default behavior of getting materials from `ob_obj.bdata.material_slots`.
-                ob_obj.override_materials = eval_mats
+                ob_obj.override_materials = tuple(eval_mats)
         elif do_convert:
             tmp_me = bpy.data.meshes.new_from_object(ob, preserve_all_data_layers=True, depsgraph=depsgraph)
         elif do_copy: