diff --git a/scripts/addons_core/bl_pkg/extensions_map_from_legacy_addons.py b/scripts/addons_core/bl_pkg/extensions_map_from_legacy_addons.py
index c7eace463cc..ea8c270de41 100644
--- a/scripts/addons_core/bl_pkg/extensions_map_from_legacy_addons.py
+++ b/scripts/addons_core/bl_pkg/extensions_map_from_legacy_addons.py
@@ -94,12 +94,5 @@
         "system_demo_mode": ("demo_mode", "Demo Mode"),
         "system_property_chart": ("property_chart", "Property Chart"),
         "vdm_brush_baker": ("vdm_brush_baker", "VDM Brush Baker"),
-
-        # These were built-in but not mapped to an extension ("install" won't be shown in the UI).
-        "io_coat3D": ("", "3D-Coat Applink"),  # External dependencies.
-        "depsgraph_debug": ("", "Dependency Graph Debug"),  # External dependencies.
-        "io_import_images_as_planes": ("", "Import Images as Planes"),  # Integrated with Blender.
-        "io_mesh_stl": ("", "STL Format"),  # Was on by default.
-        "io_scene_x3d": ("", "Web3D X3D/VRML2 format"),  # Was on by default.
     },
 }
diff --git a/source/blender/blenloader/intern/versioning_userdef.cc b/source/blender/blenloader/intern/versioning_userdef.cc
index 13c9bb015e0..8b32984afb3 100644
--- a/source/blender/blenloader/intern/versioning_userdef.cc
+++ b/source/blender/blenloader/intern/versioning_userdef.cc
@@ -982,6 +982,21 @@ void blo_do_versions_userdef(UserDef *userdef)
     BKE_preferences_extension_repo_add_default_system(userdef);
   }
 
+  if (!USER_VERSION_ATLEAST(402, 58)) {
+    /* Remove add-ons which are no longer bundled by default
+     * and have no upgrade path to extensions in the UI. */
+    const char *addon_modules[] = {
+        "depsgraph_debug",
+        "io_coat3D",
+        "io_import_images_as_planes",
+        "io_mesh_stl",
+        "io_scene_x3d",
+    };
+    for (int i = 0; i < ARRAY_SIZE(addon_modules); i++) {
+      BKE_addon_remove_safe(&userdef->addons, addon_modules[i]);
+    }
+  }
+
   /**
    * Always bump subversion in BKE_blender_version.h when adding versioning
    * code here, and wrap it inside a USER_VERSION_ATLEAST check.