diff --git a/release/scripts/modules/bpy/utils/__init__.py b/release/scripts/modules/bpy/utils/__init__.py
index 7f39cc5d422..d984a6f54a4 100644
--- a/release/scripts/modules/bpy/utils/__init__.py
+++ b/release/scripts/modules/bpy/utils/__init__.py
@@ -121,15 +121,25 @@ def _test_import(module_name, loaded_modules):
     return mod
 
 
-# Reloading would add twice.
+# Check before adding paths as reloading would add twice.
+
+# Storing and restoring the full `sys.path` is risky as this may be intentionally modified
+# by technical users/developers.
+#
+# Instead, track which paths have been added, clearing them before refreshing.
+# This supports the case of loading a new preferences file which may reset scripts path.
+_sys_path_ensure_paths = set()
+
 def _sys_path_ensure_prepend(path):
     if path not in _sys.path:
         _sys.path.insert(0, path)
+        _sys_path_ensure_paths.add(path)
 
 
 def _sys_path_ensure_append(path):
     if path not in _sys.path:
         _sys.path.append(path)
+        _sys_path_ensure_paths.add(path)
 
 
 def modules_from_path(path, loaded_modules):
@@ -391,6 +401,13 @@ def refresh_script_paths():
     Run this after creating new script paths to update sys.path
     """
 
+    for path in _sys_path_ensure_paths:
+        try:
+            _sys.path.remove(path)
+        except ValueError:
+            pass
+    _sys_path_ensure_paths.clear()
+
     for base_path in script_paths():
         for path_subdir in _script_module_dirs:
             path = _os.path.join(base_path, path_subdir)
diff --git a/source/blender/windowmanager/intern/wm_files.c b/source/blender/windowmanager/intern/wm_files.c
index 42d17387d77..090c28a81a6 100644
--- a/source/blender/windowmanager/intern/wm_files.c
+++ b/source/blender/windowmanager/intern/wm_files.c
@@ -580,7 +580,10 @@ static void wm_file_read_post(bContext *C,
 
 #ifdef WITH_PYTHON
   if (is_startup_file) {
-    /* possible python hasn't been initialized */
+    /* On startup (by default), Python won't have been initialized.
+     *
+     * The following block handles data & preferences being reloaded
+     * which requires resetting some internal variables. */
     if (CTX_py_init_get(C)) {
       bool reset_all = use_userdef;
       if (use_userdef || reset_app_template) {
@@ -592,8 +595,16 @@ static void wm_file_read_post(bContext *C,
         }
       }
       if (reset_all) {
-        /* sync addons, these may have changed from the defaults */
-        BPY_run_string_eval(C, (const char *[]){"addon_utils", NULL}, "addon_utils.reset_all()");
+        BPY_run_string_exec(
+            C,
+            (const char *[]){"bpy", "addon_utils", NULL},
+            /* Refresh scripts as the preferences may have changed the user-scripts path.
+             *
+             * This is needed when loading settings from the previous version,
+             * otherwise the script path stored in the preferences would be ignored. */
+            "bpy.utils.refresh_script_paths()\n"
+            /* Sync add-ons, these may have changed from the defaults. */
+            "addon_utils.reset_all()");
       }
       if (use_data) {
         BPY_python_reset(C);