diff --git a/rpcs3/Emu/System.cpp b/rpcs3/Emu/System.cpp
index 4d4765f962..b9a3fdbca6 100644
--- a/rpcs3/Emu/System.cpp
+++ b/rpcs3/Emu/System.cpp
@@ -1977,12 +1977,17 @@ bool Emulator::Quit(bool force_quit)
 	// The callback is only used if we actually quit RPCS3
 	const auto on_exit = []()
 	{
-		// Deinitialize object manager to prevent any hanging objects at program exit
-		g_fxo->clear();
+		Emu.CleanUp();
 	};
 	return GetCallbacks().try_to_quit(force_quit, on_exit);
 }
 
+void Emulator::CleanUp()
+{
+	// Deinitialize object manager to prevent any hanging objects at program exit
+	g_fxo->clear();
+}
+
 std::string Emulator::GetFormattedTitle(double fps) const
 {
 	rpcs3::title_format_data title_data;
diff --git a/rpcs3/Emu/System.h b/rpcs3/Emu/System.h
index a0c650d33a..b62ceff7b9 100644
--- a/rpcs3/Emu/System.h
+++ b/rpcs3/Emu/System.h
@@ -236,6 +236,7 @@ public:
 	void Stop(bool restart = false);
 	void Restart() { Stop(true); }
 	bool Quit(bool force_quit);
+	void CleanUp();
 
 	bool IsRunning() const { return m_state == system_state::running; }
 	bool IsPaused()  const { return m_state == system_state::paused; }
diff --git a/rpcs3/rpcs3qt/update_manager.cpp b/rpcs3/rpcs3qt/update_manager.cpp
index e173756ce5..4e097cbc33 100644
--- a/rpcs3/rpcs3qt/update_manager.cpp
+++ b/rpcs3/rpcs3qt/update_manager.cpp
@@ -545,6 +545,10 @@ bool update_manager::handle_rpcs3(const QByteArray& data)
 
 	QMessageBox::information(m_parent, tr("Auto-updater"), tr("Update successful!\nRPCS3 will now restart."));
 
+	Emu.SetForceBoot(true);
+	Emu.Stop();
+	Emu.CleanUp();
+
 #ifdef _WIN32
 	const int ret = _wexecl(wchar_orig_path.data(), L"--updating", nullptr);
 #else