diff --git a/core/script_language.cpp b/core/script_language.cpp
index b63aeb952cc..bb2e9a07ff1 100644
--- a/core/script_language.cpp
+++ b/core/script_language.cpp
@@ -275,7 +275,11 @@ 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 5118ccacadd..7537c866768 100644
--- a/editor/editor_data.cpp
+++ b/editor/editor_data.cpp
@@ -936,7 +936,11 @@ void EditorData::script_class_save_icon_paths() {
 		}
 	}
 
-	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();
 }