diff --git a/editor/filesystem_dock.cpp b/editor/filesystem_dock.cpp
index b8019a15e93..364a453e0aa 100644
--- a/editor/filesystem_dock.cpp
+++ b/editor/filesystem_dock.cpp
@@ -2795,6 +2795,12 @@ void FileSystemDock::_folder_color_index_pressed(int p_index, PopupMenu *p_menu)
 		}
 	}
 
+	if (!ProjectSettings::get_singleton()->has_setting("file_customization/folder_colors")) {
+		ProjectSettings::get_singleton()->set_setting("file_customization/folder_colors", assigned_folder_colors);
+	} else if (assigned_folder_colors.is_empty()) {
+		ProjectSettings::get_singleton()->set_setting("file_customization/folder_colors", Variant());
+	}
+
 	ProjectSettings::get_singleton()->save();
 
 	_update_tree(get_uncollapsed_paths());