diff --git a/core/script_language.cpp b/core/script_language.cpp
index bb2e9a07ff1..d535c54dea4 100644
--- a/core/script_language.cpp
+++ b/core/script_language.cpp
@@ -276,7 +276,9 @@ void ScriptServer::save_global_classes() {
 	}
 
 	if (gcarr.empty()) {
-		ProjectSettings::get_singleton()->clear("_global_script_classes");
+		if (ProjectSettings::get_singleton()->has_setting("_global_script_classes")) {
+			ProjectSettings::get_singleton()->clear("_global_script_classes");
+		}
 	} else {
 		ProjectSettings::get_singleton()->set("_global_script_classes", gcarr);
 	}
diff --git a/editor/editor_data.cpp b/editor/editor_data.cpp
index 7537c866768..1002c4917ba 100644
--- a/editor/editor_data.cpp
+++ b/editor/editor_data.cpp
@@ -937,7 +937,9 @@ void EditorData::script_class_save_icon_paths() {
 	}
 
 	if (d.empty()) {
-		ProjectSettings::get_singleton()->clear("_global_script_class_icons");
+		if (ProjectSettings::get_singleton()->has_setting("_global_script_class_icons")) {
+			ProjectSettings::get_singleton()->clear("_global_script_class_icons");
+		}
 	} else {
 		ProjectSettings::get_singleton()->set("_global_script_class_icons", d);
 	}