diff --git a/editor/settings/editor_autoload_settings.cpp b/editor/settings/editor_autoload_settings.cpp
index 4002af86d3c4..ec009df6b1e4 100644
--- a/editor/settings/editor_autoload_settings.cpp
+++ b/editor/settings/editor_autoload_settings.cpp
@@ -502,7 +502,7 @@ void EditorAutoloadSettings::update_autoload() {
 			if (old_info.path == info.path) {
 				// Still the same resource, check status
 				info.node = old_info.node;
-				if (info.node) {
+				if (info.node && info.node->is_instance()) {
 					Ref<Script> scr = info.node->get_script();
 					info.in_editor = scr.is_valid() && scr->is_tool();
 					if (info.is_singleton == old_info.is_singleton && info.in_editor == old_info.in_editor) {