diff --git a/desmume/src/gtk-glade/main.cpp b/desmume/src/gtk-glade/main.cpp
index db2d43456..2d8ee1451 100755
--- a/desmume/src/gtk-glade/main.cpp
+++ b/desmume/src/gtk-glade/main.cpp
@@ -525,7 +525,8 @@ common_gtk_glade_main( struct configured_features *my_config) {
         uninit_joy();
 
 	SDL_Quit();
-	desmume_config_write_file(keyfile);
+	desmume_config_update_keys(keyfile);
+	desmume_config_update_joykeys(keyfile);
 	desmume_config_dispose(keyfile);
 	return EXIT_SUCCESS;
 }