diff --git a/gtk3/main.c b/gtk3/main.c
index 6cdfddc..4d3ea40 100644
--- a/gtk3/main.c
+++ b/gtk3/main.c
@@ -54,6 +54,7 @@ typedef struct GuiData {
 
 	GFile *file;
 	gint sample_rate;
+	GDateTime *config_modification_date;
 
 	char *battery_save_path;
 	char *cheats_save_path;
@@ -1615,7 +1616,14 @@ static void run(void) {
 //
 // TODO: Make sure we have a way to quit our emulation loop before `shutdown` gets called
 static void quit(void) {
+	g_debug("quit(void);");
+
 	stop();
+	while (gui_data.stopping);
+
+	GtkWindow *window = gui_data.main_window ? GTK_WINDOW(gui_data.main_window) : NULL;
+	save_settings(window, gui_data.config_modification_date);
+	free_settings();
 
 	for (unsigned i = 0; i < gui_data.controller_count; i++) {
 		struct Controller_t *s = &gui_data.controllers[i];
@@ -1630,12 +1638,16 @@ static void quit(void) {
 }
 
 static void quit_interrupt(int ignored) {
+	g_debug("quit_interrupt(%d);", ignored);
+
 	quit();
 }
 
 // `destroy` signal GCallback
 // Exits the application
 static void on_quit(GtkWidget *w, gpointer app) {
+	g_debug("on_quit(%p, %p);", w, &app);
+
 	quit();
 }
 
@@ -1994,7 +2006,7 @@ static void startup(GApplication *app, gpointer null_ptr) {
 	gui_data.preferences = GTK_WINDOW(get_object("preferences"));
 
 	g_signal_connect(gui_data.preferences, "realize", G_CALLBACK(on_preferences_realize), (gpointer) gui_data.builder);
-	init_settings(app, gui_data.cli_options.config_path, gui_data.preferences);
+	init_settings(app, gui_data.cli_options.config_path, &gui_data.config_modification_date, gui_data.preferences);
 
 	gui_data.vram_viewer = GTK_WINDOW(get_object("vram_viewer"));
 	gui_data.memory_viewer = GTK_WINDOW(get_object("memory_viewer"));
@@ -2311,11 +2323,6 @@ static void shutdown(GApplication *app, GFile **files, gint n_files, const gchar
 
 	stop();
 	while (gui_data.stopping);
-
-	g_object_unref(gui_data.builder);
-
-	save_settings();
-	free_settings();
 	SDL_Quit();
 
 	if (gui_data.image_buffers[0]) g_free(gui_data.image_buffers[0]);
@@ -2325,6 +2332,8 @@ static void shutdown(GApplication *app, GFile **files, gint n_files, const gchar
 	free_master_shader();
 
 	GB_free(&gb);
+	
+	g_object_unref(gui_data.builder);
 }
 
 // This function gets called when there are files to open.
diff --git a/gtk3/settings.c b/gtk3/settings.c
index f763828..c399b45 100644
--- a/gtk3/settings.c
+++ b/gtk3/settings.c
@@ -3,6 +3,9 @@
 #define get_object(id) gtk_builder_get_object(builder, id)
 #define builder_get(type, id) type(get_object(id))
 
+gchar* settings_file_path;
+GKeyFile *key_file;
+
 static void print_config_error(GError *error) {
 	if (error == NULL) return;
 
@@ -108,6 +111,13 @@ void save_config_to_key_file(config_t *config, GKeyFile *key_file) {
 	#undef EXPAND_GROUP_MEMBER_IF_EVAL
 	#undef EXPAND_GROUP_MEMBER_IF_0
 	#undef EXPAND_GROUP_MEMBER_IF_1
+
+	// Save config to disk
+	if (!g_key_file_save_to_file(key_file, settings_file_path, &error)) {
+		g_warning ("Failed to save %s: %s", settings_file_path, error->message);
+		g_error_free(error);
+		return;
+	}
 }
 
 void on_preferences_realize(GtkWidget *w, gpointer builder_ptr) {
@@ -147,7 +157,7 @@ void on_preferences_realize(GtkWidget *w, gpointer builder_ptr) {
 	#endif
 }
 
-void init_settings(GApplication *app, gchar *path, GtkWindow *preferences) {
+void init_settings(GApplication *app, gchar *path, GDateTime **modification_date, GtkWindow *preferences) {
 	free_settings();
 	key_file = g_key_file_new();
 
@@ -158,14 +168,18 @@ void init_settings(GApplication *app, gchar *path, GtkWindow *preferences) {
 		settings_file_path = g_build_filename(g_get_user_config_dir(), SETTINGS_FILE, NULL);
 	}
 
-	load_settings(app);
+	load_settings(app, modification_date);
 }
 
-int load_settings(GApplication *app) {
+int load_settings(GApplication *app, GDateTime **modification_date) {
 	GError *error = NULL;
 
 	g_message("Trying to load settings from %s", settings_file_path);
 
+	g_autoptr(GFile) file = g_file_new_for_path(settings_file_path);
+	g_autoptr(GFileInfo) file_info = g_file_query_info(file, "time::*", G_FILE_QUERY_INFO_NONE, NULL, NULL);
+	*modification_date = g_file_info_get_modification_date_time(file_info);
+
 	if (!g_key_file_load_from_file(key_file, settings_file_path, G_KEY_FILE_KEEP_COMMENTS | G_KEY_FILE_KEEP_TRANSLATIONS, &error)) {
 		if (error->domain == G_FILE_ERROR) {
 			g_warning("Unable to load %s: %s", settings_file_path, error->message);
@@ -186,17 +200,40 @@ int load_settings(GApplication *app) {
 	return 0;
 }
 
-void save_settings(void) {
+void save_settings(GtkWindow *main_window, GDateTime *saved_modification_date) {
 	GError *error = NULL;
 
 	g_message("Trying to save settings to %s", settings_file_path);
 	
-	save_config_to_key_file(&config, key_file);
+	g_autoptr(GFile) file = g_file_new_for_path(settings_file_path);
+	g_autoptr(GFileInfo) file_info = g_file_query_info(file, "time::*", G_FILE_QUERY_INFO_NONE, NULL, NULL);
+	GDateTime *modification_date = g_file_info_get_modification_date_time(file_info);
 
-	if (!g_key_file_save_to_file(key_file, settings_file_path, &error)) {
-		g_warning ("Failed to save %s: %s", settings_file_path, error->message);
-		g_error_free(error);
-		return;
+	if (!g_date_time_equal(saved_modification_date, modification_date)) {
+		GtkMessageDialog *dialog = GTK_MESSAGE_DIALOG(gtk_message_dialog_new(
+			main_window,
+			GTK_DIALOG_MODAL | GTK_DIALOG_DESTROY_WITH_PARENT,
+			GTK_MESSAGE_QUESTION,
+			GTK_BUTTONS_YES_NO,
+			"It looks like the configuration has changed on disk. Overwrite?"
+		));
+
+		gtk_window_set_title(GTK_WINDOW(dialog), "SameBoy");
+
+		gint result = gtk_dialog_run(GTK_DIALOG(dialog));
+
+		switch (result) {
+			case GTK_RESPONSE_YES:
+				save_config_to_key_file(&config, key_file);
+			break;
+
+			default:
+				// Action has been canceled
+			break;
+		}
+	}
+	else {
+		save_config_to_key_file(&config, key_file);
 	}
 }
 
diff --git a/gtk3/settings.h b/gtk3/settings.h
index 60e153f..0caf1a4 100644
--- a/gtk3/settings.h
+++ b/gtk3/settings.h
@@ -76,8 +76,6 @@ enum menubar_type_t {
 	MENUBAR_SHOW_HAMBURGER
 };
 
-gchar* settings_file_path;
-GKeyFile *key_file;
 config_t config;
 
 void on_preferences_realize(GtkWidget *w, gpointer builder_ptr);
@@ -85,9 +83,9 @@ void on_preferences_realize(GtkWidget *w, gpointer builder_ptr);
 void print_config(config_t *config);
 void load_config_from_key_file(config_t *config, GKeyFile *key_file);
 
-void init_settings(GApplication *app, gchar *path, GtkWindow *preferences);
-int load_settings(GApplication *app);
-void save_settings(void);
+void init_settings(GApplication *app, gchar *path, GDateTime **modification_date, GtkWindow *preferences);
+int load_settings(GApplication *app, GDateTime **modification_date);
+void save_settings(GtkWindow *main_window, GDateTime *saved_modification_date);
 void free_settings(void);
 
 void update_boot_rom_selector(GtkBuilder *builder);