diff --git a/source/blender/windowmanager/WM_api.hh b/source/blender/windowmanager/WM_api.hh
index bc7786a8779..c810ea65725 100644
--- a/source/blender/windowmanager/WM_api.hh
+++ b/source/blender/windowmanager/WM_api.hh
@@ -423,9 +423,20 @@ void WM_window_decoration_style_apply(const wmWindow *win, const bScreen *screen
 /* `wm_files.cc`. */
 
 void WM_file_autoexec_init(const char *filepath);
-bool WM_file_read(bContext *C, const char *filepath, ReportList *reports);
+/**
+ * \param use_scripts_autoexec_check: When true, script auto-execution checks excluded directories.
+ * Note that this is passed in as an argument because `filepath` may reference a path to recover.
+ * In this case the that used for exclusion is the recovery path which is only known once
+ * the file has been loaded.
+ */
+bool WM_file_read(bContext *C,
+                  const char *filepath,
+                  const bool use_scripts_autoexec_check,
+                  ReportList *reports);
 void WM_file_autosave_init(wmWindowManager *wm);
-bool WM_file_recover_last_session(bContext *C, ReportList *reports);
+bool WM_file_recover_last_session(bContext *C,
+                                  const bool use_scripts_autoexec_check,
+                                  ReportList *reports);
 void WM_file_tag_modified();
 
 /**
diff --git a/source/blender/windowmanager/intern/wm_files.cc b/source/blender/windowmanager/intern/wm_files.cc
index e2ef05792ad..ac7c032a313 100644
--- a/source/blender/windowmanager/intern/wm_files.cc
+++ b/source/blender/windowmanager/intern/wm_files.cc
@@ -1043,7 +1043,10 @@ static void file_read_reports_finalize(BlendFileReadReport *bf_reports)
   bf_reports->resynced_lib_overrides_libraries = nullptr;
 }
 
-bool WM_file_read(bContext *C, const char *filepath, ReportList *reports)
+bool WM_file_read(bContext *C,
+                  const char *filepath,
+                  const bool use_scripts_autoexec_check,
+                  ReportList *reports)
 {
   /* Assume automated tasks with background, don't write recent file list. */
   const bool do_history_file_update = (G.background == false) &&
@@ -1110,6 +1113,14 @@ bool WM_file_read(bContext *C, const char *filepath, ReportList *reports)
         G.f = (G.f & ~flags_keep) | (G_f_orig & flags_keep);
       }
 
+      /* Set by the `use_scripts` property on file load.
+       * If this was not set, then it should be calculated based on the file-path.
+       * Note that this uses `bmain->filepath` and not `filepath`, necessary when
+       * recovering the last session, where the file-path can be #BLENDER_QUIT_FILE. */
+      if (use_scripts_autoexec_check) {
+        WM_file_autoexec_init(bmain->filepath);
+      }
+
       WM_check(C); /* Opens window(s), checks keymaps. */
 
       if (do_history_file_update) {
@@ -2459,9 +2470,10 @@ void wm_open_init_load_ui(wmOperator *op, bool use_prefs)
   }
 }
 
-void wm_open_init_use_scripts(wmOperator *op, bool use_prefs)
+bool wm_open_init_use_scripts(wmOperator *op, bool use_prefs)
 {
   PropertyRNA *prop = RNA_struct_find_property(op->ptr, "use_scripts");
+  bool use_scripts_autoexec_check = false;
   if (!RNA_property_is_set(op->ptr, prop)) {
     /* Use #G_FLAG_SCRIPT_AUTOEXEC rather than the userpref because this means if
      * the flag has been disabled from the command line, then opening
@@ -2470,7 +2482,9 @@ void wm_open_init_use_scripts(wmOperator *op, bool use_prefs)
                              ((G.f & G_FLAG_SCRIPT_AUTOEXEC) != 0);
 
     RNA_property_boolean_set(op->ptr, prop, value);
+    use_scripts_autoexec_check = true;
   }
+  return use_scripts_autoexec_check;
 }
 
 /** \} */
@@ -3065,18 +3079,16 @@ void WM_OT_read_factory_settings(wmOperatorType *ot)
 /**
  * Wrap #WM_file_read, shared by file reading operators.
  */
-static bool wm_file_read_opwrap(bContext *C, const char *filepath, ReportList *reports)
+static bool wm_file_read_opwrap(bContext *C,
+                                const char *filepath,
+                                const bool use_scripts_autoexec_check,
+                                ReportList *reports)
 {
   /* XXX: wm in context is not set correctly after #WM_file_read -> crash. */
   /* Do it before for now, but is this correct with multiple windows? */
   WM_event_add_notifier(C, NC_WINDOW, nullptr);
 
-  /* Set by the "use_scripts" property on file load. */
-  if ((G.f & G_FLAG_SCRIPT_AUTOEXEC) == 0) {
-    WM_file_autoexec_init(filepath);
-  }
-
-  const bool success = WM_file_read(C, filepath, reports);
+  const bool success = WM_file_read(C, filepath, use_scripts_autoexec_check, reports);
 
   return success;
 }
@@ -3179,7 +3191,8 @@ static wmOperatorStatus wm_open_mainfile__select_file_path_exec(bContext *C, wmO
 
   RNA_string_set(op->ptr, "filepath", blendfile_path);
   wm_open_init_load_ui(op, true);
-  wm_open_init_use_scripts(op, true);
+  const bool use_scripts_autoexec_check = wm_open_init_use_scripts(op, true);
+  UNUSED_VARS(use_scripts_autoexec_check); /* The user can set this in the UI. */
   op->customdata = nullptr;
 
   WM_event_add_fileselect(C, op);
@@ -3200,11 +3213,11 @@ static wmOperatorStatus wm_open_mainfile__open(bContext *C, wmOperator *op)
 
   /* Re-use last loaded setting so we can reload a file without changing. */
   wm_open_init_load_ui(op, false);
-  wm_open_init_use_scripts(op, false);
+  const bool use_scripts_autoexec_check = wm_open_init_use_scripts(op, false);
 
   SET_FLAG_FROM_TEST(G.fileflags, !RNA_boolean_get(op->ptr, "load_ui"), G_FILE_NO_UI);
   SET_FLAG_FROM_TEST(G.f, RNA_boolean_get(op->ptr, "use_scripts"), G_FLAG_SCRIPT_AUTOEXEC);
-  success = wm_file_read_opwrap(C, filepath, op->reports);
+  success = wm_file_read_opwrap(C, filepath, use_scripts_autoexec_check, op->reports);
 
   if (success) {
     if (G.fileflags & G_FILE_NO_UI) {
@@ -3410,12 +3423,12 @@ static wmOperatorStatus wm_revert_mainfile_exec(bContext *C, wmOperator *op)
   bool success;
   char filepath[FILE_MAX];
 
-  wm_open_init_use_scripts(op, false);
+  const bool use_scripts_autoexec_check = wm_open_init_use_scripts(op, false);
 
   SET_FLAG_FROM_TEST(G.f, RNA_boolean_get(op->ptr, "use_scripts"), G_FLAG_SCRIPT_AUTOEXEC);
 
   STRNCPY(filepath, BKE_main_blendfile_path(bmain));
-  success = wm_file_read_opwrap(C, filepath, op->reports);
+  success = wm_file_read_opwrap(C, filepath, use_scripts_autoexec_check, op->reports);
 
   if (success) {
     return OPERATOR_FINISHED;
@@ -3448,21 +3461,24 @@ void WM_OT_revert_mainfile(wmOperatorType *ot)
 /** \name Recover Last Session Operator
  * \{ */
 
-bool WM_file_recover_last_session(bContext *C, ReportList *reports)
+bool WM_file_recover_last_session(bContext *C,
+                                  const bool use_scripts_autoexec_check,
+                                  ReportList *reports)
 {
   char filepath[FILE_MAX];
   BLI_path_join(filepath, sizeof(filepath), BKE_tempdir_base(), BLENDER_QUIT_FILE);
   G.fileflags |= G_FILE_RECOVER_READ;
-  const bool success = wm_file_read_opwrap(C, filepath, reports);
+  const bool success = wm_file_read_opwrap(C, filepath, use_scripts_autoexec_check, reports);
   G.fileflags &= ~G_FILE_RECOVER_READ;
   return success;
 }
 
-static wmOperatorStatus wm_recover_last_session_exec(bContext *C, wmOperator *op)
+static wmOperatorStatus wm_recover_last_session_impl(bContext *C,
+                                                     wmOperator *op,
+                                                     const bool use_scripts_autoexec_check)
 {
-  wm_open_init_use_scripts(op, true);
   SET_FLAG_FROM_TEST(G.f, RNA_boolean_get(op->ptr, "use_scripts"), G_FLAG_SCRIPT_AUTOEXEC);
-  if (WM_file_recover_last_session(C, op->reports)) {
+  if (WM_file_recover_last_session(C, use_scripts_autoexec_check, op->reports)) {
     if (!G.background) {
       wmOperatorType *ot = op->type;
       PointerRNA *props_ptr = MEM_new<PointerRNA>(__func__);
@@ -3475,6 +3491,12 @@ static wmOperatorStatus wm_recover_last_session_exec(bContext *C, wmOperator *op
   return OPERATOR_CANCELLED;
 }
 
+static wmOperatorStatus wm_recover_last_session_exec(bContext *C, wmOperator *op)
+{
+  const bool use_scripts_autoexec_check = wm_open_init_use_scripts(op, true);
+  return wm_recover_last_session_impl(C, op, use_scripts_autoexec_check);
+}
+
 static void wm_recover_last_session_after_dialog_callback(bContext *C, void *user_data)
 {
   WM_operator_name_call_with_properties(
@@ -3487,14 +3509,14 @@ static wmOperatorStatus wm_recover_last_session_invoke(bContext *C,
 {
   /* Keep the current setting instead of using the preferences since a file selector
    * doesn't give us the option to change the setting. */
-  wm_open_init_use_scripts(op, false);
+  const bool use_scripts_autoexec_check = wm_open_init_use_scripts(op, false);
 
   if (wm_operator_close_file_dialog_if_needed(
           C, op, wm_recover_last_session_after_dialog_callback))
   {
     return OPERATOR_INTERFACE;
   }
-  return wm_recover_last_session_exec(C, op);
+  return wm_recover_last_session_impl(C, op, use_scripts_autoexec_check);
 }
 
 void WM_OT_recover_last_session(wmOperatorType *ot)
@@ -3523,12 +3545,12 @@ static wmOperatorStatus wm_recover_auto_save_exec(bContext *C, wmOperator *op)
   RNA_string_get(op->ptr, "filepath", filepath);
   BLI_path_canonicalize_native(filepath, sizeof(filepath));
 
-  wm_open_init_use_scripts(op, true);
+  const bool use_scripts_autoexec_check = wm_open_init_use_scripts(op, true);
   SET_FLAG_FROM_TEST(G.f, RNA_boolean_get(op->ptr, "use_scripts"), G_FLAG_SCRIPT_AUTOEXEC);
 
   G.fileflags |= G_FILE_RECOVER_READ;
 
-  success = wm_file_read_opwrap(C, filepath, op->reports);
+  success = wm_file_read_opwrap(C, filepath, use_scripts_autoexec_check, op->reports);
 
   G.fileflags &= ~G_FILE_RECOVER_READ;
 
@@ -3553,7 +3575,8 @@ static wmOperatorStatus wm_recover_auto_save_invoke(bContext *C,
 
   wm_autosave_location(filepath);
   RNA_string_set(op->ptr, "filepath", filepath);
-  wm_open_init_use_scripts(op, true);
+  const bool use_scripts_autoexec_check = wm_open_init_use_scripts(op, true);
+  UNUSED_VARS(use_scripts_autoexec_check); /* The user can set this in the UI. */
   WM_event_add_fileselect(C, op);
 
   return OPERATOR_RUNNING_MODAL;
diff --git a/source/blender/windowmanager/wm.hh b/source/blender/windowmanager/wm.hh
index d6d71fb0966..4db8925d996 100644
--- a/source/blender/windowmanager/wm.hh
+++ b/source/blender/windowmanager/wm.hh
@@ -8,6 +8,8 @@
 
 #pragma once
 
+#include "BLI_compiler_attrs.h"
+
 struct wmOperator;
 struct wmTimer;
 struct wmWindow;
@@ -119,4 +121,7 @@ void wm_stereo3d_set_cancel(bContext *C, wmOperator *op);
  * Initialize operator properties.
  */
 void wm_open_init_load_ui(wmOperator *op, bool use_prefs);
-void wm_open_init_use_scripts(wmOperator *op, bool use_prefs);
+/**
+ * Return true if the script auto-execution should be cleared based on #WM_file_autoexec_init.
+ */
+bool wm_open_init_use_scripts(wmOperator *op, bool use_prefs) ATTR_WARN_UNUSED_RESULT;
diff --git a/source/creator/creator_args.cc b/source/creator/creator_args.cc
index a7e5f0e7702..42d472a9235 100644
--- a/source/creator/creator_args.cc
+++ b/source/creator/creator_args.cc
@@ -2535,8 +2535,11 @@ static bool handle_load_file(bContext *C, const char *filepath_arg, const bool l
   /* Load the file. */
   ReportList reports;
   BKE_reports_init(&reports, RPT_PRINT);
-  WM_file_autoexec_init(filepath);
-  const bool success = WM_file_read(C, filepath, &reports);
+  /* When activating from the command line there isn't an exact equivalent to operator properties.
+   * Instead, enabling auto-execution via `--enable-autoexec` causes the auto-execution
+   * check to be skipped (if it's set), so it's fine to always enable the check here. */
+  const bool use_scripts_autoexec_check = true;
+  const bool success = WM_file_read(C, filepath, use_scripts_autoexec_check, &reports);
   BKE_reports_free(&reports);
 
   if (success) {