diff --git a/editor/settings/editor_settings.cpp b/editor/settings/editor_settings.cpp
index 0412cdaebca..5ddf60ab8b1 100644
--- a/editor/settings/editor_settings.cpp
+++ b/editor/settings/editor_settings.cpp
@@ -1955,7 +1955,6 @@ void EditorSettings::add_shortcut(const String &p_path, const Ref<Shortcut> &p_s
 		p_shortcut->set_name(shortcut_name);
 	}
 	shortcuts[p_path] = p_shortcut;
-	shortcuts[p_path]->set_meta("customized", true);
 }
 
 void EditorSettings::remove_shortcut(const String &p_path) {
@@ -2084,7 +2083,7 @@ void ED_SHORTCUT_OVERRIDE_ARRAY(const String &p_path, const String &p_feature, c
 	}
 
 	// Override the existing shortcut only if it wasn't customized by the user.
-	if (!sc->has_meta("customized")) {
+	if (Shortcut::is_event_array_equal(sc->get_events(), sc->get_meta("original"))) {
 		sc->set_events(events);
 	}