diff --git a/core/script_language.cpp b/core/script_language.cpp
index 7392e7a0afc..96313898ec4 100644
--- a/core/script_language.cpp
+++ b/core/script_language.cpp
@@ -276,7 +276,11 @@ void ScriptServer::save_global_classes() {
 		gcarr.push_back(d);
 	}
 
-	ProjectSettings::get_singleton()->set("_global_script_classes", gcarr);
+	if (gcarr.empty()) {
+		ProjectSettings::get_singleton()->clear("_global_script_classes");
+	} else {
+		ProjectSettings::get_singleton()->set("_global_script_classes", gcarr);
+	}
 	ProjectSettings::get_singleton()->save();
 }
 
diff --git a/editor/editor_data.cpp b/editor/editor_data.cpp
index 01cc23aaa29..93486860a77 100644
--- a/editor/editor_data.cpp
+++ b/editor/editor_data.cpp
@@ -965,7 +965,11 @@ void EditorData::script_class_save_icon_paths() {
 			d[E->get()] = _script_class_icon_paths[E->get()];
 	}
 
-	ProjectSettings::get_singleton()->set("_global_script_class_icons", d);
+	if (d.empty()) {
+		ProjectSettings::get_singleton()->clear("_global_script_class_icons");
+	} else {
+		ProjectSettings::get_singleton()->set("_global_script_class_icons", d);
+	}
 	ProjectSettings::get_singleton()->save();
 }