diff --git a/rpcs3/Emu/System.cpp b/rpcs3/Emu/System.cpp
index 9566939b62..0c5c403f7c 100644
--- a/rpcs3/Emu/System.cpp
+++ b/rpcs3/Emu/System.cpp
@@ -1963,13 +1963,11 @@ void Emulator::Stop(bool restart)
 	}
 
 	m_force_boot = false;
-	Init();
 }
 
 bool Emulator::Quit(bool force_quit)
 {
 	m_force_boot = false;
-	Emu.Stop();
 
 	// Deinitialize object manager to prevent any hanging objects at program exit
 	*g_fxo = {};
diff --git a/rpcs3/rpcs3qt/main_window.cpp b/rpcs3/rpcs3qt/main_window.cpp
index f181d3912b..26f8a7a3f8 100644
--- a/rpcs3/rpcs3qt/main_window.cpp
+++ b/rpcs3/rpcs3qt/main_window.cpp
@@ -2227,6 +2227,7 @@ void main_window::closeEvent(QCloseEvent* closeEvent)
 	}
 
 	// Cleanly stop and quit the emulator.
+	Emu.Stop();
 	Emu.Quit(true);
 }