diff --git a/src/citra_qt/game_list.cpp b/src/citra_qt/game_list.cpp
index f630a1ec2..4d1f9ab67 100644
--- a/src/citra_qt/game_list.cpp
+++ b/src/citra_qt/game_list.cpp
@@ -37,6 +37,10 @@ GameList::GameList(QWidget* parent) : QWidget{parent} {
     item_model->setHeaderData(COLUMN_FILE_TYPE, Qt::Horizontal, "File type");
     item_model->setHeaderData(COLUMN_SIZE, Qt::Horizontal, "Size");
 
+    recursive = UISettings::values.gamedir_deepscan;
+    game_directory = UISettings::values.gamedir;
+    PopulateAsync(game_directory, recursive);
+
     connect(tree_view, &QTreeView::activated, this, &GameList::ValidateEntry);
     connect(tree_view, &QTreeView::customContextMenuRequested, this, &GameList::PopupContextMenu);
     connect(&watcher, &QFileSystemWatcher::directoryChanged, this, &GameList::RefreshGameDirectory);
@@ -151,9 +155,18 @@ static bool HasSupportedFileExtension(const std::string& file_name) {
 }
 
 void GameList::RefreshGameDirectory() {
-    if (!UISettings::values.gamedir.isEmpty() && current_worker != nullptr) {
+    if (!game_directory.isEmpty() && current_worker != nullptr) {
         LOG_INFO(Frontend, "Change detected in the games directory. Reloading game list.");
-        PopulateAsync(UISettings::values.gamedir, UISettings::values.gamedir_deepscan);
+        PopulateAsync(game_directory, recursive);
+    }
+}
+
+void GameList::OnSettingsUpdated() {
+    if (UISettings::values.gamedir_deepscan != recursive ||
+        UISettings::values.gamedir != game_directory) {
+        game_directory = UISettings::values.gamedir;
+        recursive = UISettings::values.gamedir_deepscan;
+        RefreshGameDirectory();
     }
 }
 
diff --git a/src/citra_qt/game_list.h b/src/citra_qt/game_list.h
index b141fa3a5..d0b9d44bc 100644
--- a/src/citra_qt/game_list.h
+++ b/src/citra_qt/game_list.h
@@ -33,6 +33,7 @@ public:
 
     void SaveInterfaceLayout();
     void LoadInterfaceLayout();
+    void OnSettingsUpdated();
 
     static const QStringList supported_file_extensions;
 
@@ -54,4 +55,6 @@ private:
     QStandardItemModel* item_model = nullptr;
     GameListWorker* current_worker = nullptr;
     QFileSystemWatcher watcher;
+    QString game_directory;
+    bool recursive;
 };
diff --git a/src/citra_qt/main.cpp b/src/citra_qt/main.cpp
index 2723a0217..7e0e630d2 100644
--- a/src/citra_qt/main.cpp
+++ b/src/citra_qt/main.cpp
@@ -73,8 +73,6 @@ GMainWindow::GMainWindow() : config(new Config()), emu_thread(nullptr) {
                        .arg(Common::g_build_name, Common::g_scm_branch, Common::g_scm_desc));
     show();
 
-    game_list->PopulateAsync(UISettings::values.gamedir, UISettings::values.gamedir_deepscan);
-
     QStringList args = QApplication::arguments();
     if (args.length() >= 2) {
         BootGame(args[1]);
@@ -538,7 +536,7 @@ void GMainWindow::OnMenuSelectGameListRoot() {
     QString dir_path = QFileDialog::getExistingDirectory(this, tr("Select Directory"));
     if (!dir_path.isEmpty()) {
         UISettings::values.gamedir = dir_path;
-        game_list->PopulateAsync(dir_path, UISettings::values.gamedir_deepscan);
+        game_list->OnSettingsUpdated();
     }
 }
 
@@ -612,6 +610,7 @@ void GMainWindow::OnConfigure() {
     auto result = configureDialog.exec();
     if (result == QDialog::Accepted) {
         configureDialog.applyConfiguration();
+        game_list->OnSettingsUpdated();
         config->Save();
     }
 }