diff --git a/src/duckstation-qt/mainwindow.cpp b/src/duckstation-qt/mainwindow.cpp
index 0c79d1ae5..d66ddaeef 100644
--- a/src/duckstation-qt/mainwindow.cpp
+++ b/src/duckstation-qt/mainwindow.cpp
@@ -3047,7 +3047,10 @@ void MainWindow::checkForSettingChanges()
   }
 
   LogWindow::updateSettings();
-  updateWindowState();
+
+  // don't refresh window state while setup wizard is running, i.e. no game and hidden
+  if (isVisible() || s_system_valid || s_system_starting)
+    updateWindowState();
 }
 
 std::optional<WindowInfo> MainWindow::getWindowInfo()