diff --git a/src/duckstation-qt/mainwindow.cpp b/src/duckstation-qt/mainwindow.cpp
index 2e9392d48..398c1d506 100644
--- a/src/duckstation-qt/mainwindow.cpp
+++ b/src/duckstation-qt/mainwindow.cpp
@@ -588,8 +588,7 @@ void MainWindow::onSystemDestroyed()
   // If we're closing or in batch mode, quit the whole application now.
   if (m_is_closing || QtHost::InBatchMode())
   {
-    QApplication::processEvents(QEventLoop::ExcludeUserInputEvents, 1);
-    QCoreApplication::quit();
+    quit();
     return;
   }
 
@@ -701,6 +700,22 @@ std::string MainWindow::getDeviceDiscPath(const QString& title)
   return ret;
 }
 
+void MainWindow::quit()
+{
+  // Make sure VM is gone. It really should be if we're here.
+  if (s_system_valid)
+  {
+    g_emu_thread->shutdownSystem(false);
+    while (s_system_valid)
+      QApplication::processEvents(QEventLoop::ExcludeUserInputEvents, 1);
+  }
+
+  // Ensure subwindows are removed before quitting. That way the log window cancelling
+  // the close event won't cancel the quit process.
+  destroySubWindows();
+  QGuiApplication::quit();
+}
+
 void MainWindow::recreate()
 {
   const bool was_display_created = m_display_created;
@@ -2786,7 +2801,7 @@ void MainWindow::requestExit(bool allow_confirm /* = true */)
   if (s_system_valid)
     m_is_closing = true;
   else
-    QGuiApplication::quit();
+    quit();
 }
 
 void MainWindow::checkForSettingChanges()
diff --git a/src/duckstation-qt/mainwindow.h b/src/duckstation-qt/mainwindow.h
index a2d771bdf..732f855c8 100644
--- a/src/duckstation-qt/mainwindow.h
+++ b/src/duckstation-qt/mainwindow.h
@@ -87,6 +87,9 @@ public:
   /// Locks the system by pausing it, while a popup dialog is displayed.
   SystemLock pauseAndLockSystem();
 
+  /// Force quits the application.
+  void quit();
+
   /// Accessors for the status bar widgets, updated by the emulation thread.
   ALWAYS_INLINE QLabel* getStatusRendererWidget() const { return m_status_renderer_widget; }
   ALWAYS_INLINE QLabel* getStatusResolutionWidget() const { return m_status_resolution_widget; }