diff --git a/pcsx2-qt/MainWindow.cpp b/pcsx2-qt/MainWindow.cpp
index 1489972d47..484c2d9697 100644
--- a/pcsx2-qt/MainWindow.cpp
+++ b/pcsx2-qt/MainWindow.cpp
@@ -264,7 +264,7 @@ void MainWindow::setupAdditionalUi()
 		connect(action, &QAction::triggered, [scale]() { g_emu_thread->requestDisplaySize(static_cast<float>(scale)); });
 	}
 
-	updateEmulationActions(false, false);
+	updateEmulationActions(false, false, false);
 	updateDisplayRelatedActions(false, false, false);
 
 #ifdef ENABLE_RAINTEGRATION
@@ -1085,13 +1085,13 @@ void MainWindow::restoreStateFromConfig()
 	}
 }
 
-void MainWindow::updateEmulationActions(bool starting, bool running)
+void MainWindow::updateEmulationActions(bool starting, bool running, bool stopping)
 {
 	const bool starting_or_running = starting || running;
 
-	m_ui.actionStartFile->setDisabled(starting_or_running);
-	m_ui.actionStartDisc->setDisabled(starting_or_running);
-	m_ui.actionStartBios->setDisabled(starting_or_running);
+	m_ui.actionStartFile->setDisabled(starting_or_running || stopping);
+	m_ui.actionStartDisc->setDisabled(starting_or_running || stopping);
+	m_ui.actionStartBios->setDisabled(starting_or_running || stopping);
 
 	m_ui.actionPowerOff->setEnabled(running);
 	m_ui.actionPowerOffWithoutSaving->setEnabled(running);
@@ -1116,8 +1116,8 @@ void MainWindow::updateEmulationActions(bool starting, bool running)
 		m_ui.actionPause->setChecked(false);
 
 	// scanning needs to be disabled while running
-	m_ui.actionScanForNewGames->setDisabled(starting_or_running);
-	m_ui.actionRescanAllGames->setDisabled(starting_or_running);
+	m_ui.actionScanForNewGames->setDisabled(starting_or_running || stopping);
+	m_ui.actionRescanAllGames->setDisabled(starting_or_running || stopping);
 }
 
 void MainWindow::updateDisplayRelatedActions(bool has_surface, bool render_to_main, bool fullscreen)
@@ -1371,6 +1371,14 @@ bool MainWindow::requestShutdown(bool allow_confirm, bool allow_save_to_state, b
 	if (!isRenderingToMain() && isHidden() && !QtHost::InBatchMode() && !g_emu_thread->isRunningFullscreenUI())
 		updateWindowState(true);
 
+	// Clear the VM valid state early. That way we can't do anything in the UI if we take a while to shut down.
+	if (s_vm_valid)
+	{
+		s_vm_valid = false;
+		updateEmulationActions(false, false, true);
+		updateDisplayRelatedActions(false, false, false);
+	}
+
 	// Now we can actually shut down the VM.
 	g_emu_thread->shutdownVM(save_state);
 	return true;
@@ -1916,7 +1924,7 @@ void MainWindow::onInputRecOpenViewer()
 void MainWindow::onVMStarting()
 {
 	s_vm_valid = true;
-	updateEmulationActions(true, false);
+	updateEmulationActions(true, false, false);
 	updateWindowTitle();
 
 	// prevent loading state until we're fully initialized
@@ -1927,7 +1935,7 @@ void MainWindow::onVMStarted()
 {
 	s_vm_valid = true;
 	m_was_disc_change_request = false;
-	updateEmulationActions(true, true);
+	updateEmulationActions(true, true, false);
 	updateWindowTitle();
 	updateStatusBarWidgetVisibility();
 	updateInputRecordingActions(true);
@@ -1976,7 +1984,7 @@ void MainWindow::onVMStopped()
 	s_vm_valid = false;
 	s_vm_paused = false;
 	m_last_fps_status = QString();
-	updateEmulationActions(false, false);
+	updateEmulationActions(false, false, false);
 	updateWindowTitle();
 	updateWindowState();
 	updateStatusBarWidgetVisibility();
diff --git a/pcsx2-qt/MainWindow.h b/pcsx2-qt/MainWindow.h
index a7554b1eb3..1c7ae85d6c 100644
--- a/pcsx2-qt/MainWindow.h
+++ b/pcsx2-qt/MainWindow.h
@@ -213,7 +213,7 @@ private:
 	void saveStateToConfig();
 	void restoreStateFromConfig();
 
-	void updateEmulationActions(bool starting, bool running);
+	void updateEmulationActions(bool starting, bool running, bool stopping);
 	void updateDisplayRelatedActions(bool has_surface, bool render_to_main, bool fullscreen);
 	void updateStatusBarWidgetVisibility();
 	void updateWindowTitle();