diff --git a/rpcs3/Emu/System.cpp b/rpcs3/Emu/System.cpp
index 0d7578a867..2575931393 100644
--- a/rpcs3/Emu/System.cpp
+++ b/rpcs3/Emu/System.cpp
@@ -1957,9 +1957,12 @@ void Emulator::Stop(bool restart)
 	// Always Enable display sleep, not only if it was prevented.
 	enable_display_sleep();
 
-	if (!m_force_boot && Quit(g_cfg.misc.autoexit.get()))
+	if (!m_force_boot)
 	{
-		return;
+		if (Quit(g_cfg.misc.autoexit.get()))
+		{
+			return;
+		}
 	}
 
 	m_force_boot = false;
diff --git a/rpcs3/Emu/System.h b/rpcs3/Emu/System.h
index 4839ff7a62..e24a564a8d 100644
--- a/rpcs3/Emu/System.h
+++ b/rpcs3/Emu/System.h
@@ -83,7 +83,12 @@ class Emulator final
 	u32 m_usrid{1};
 
 	bool m_force_global_config = false;
+
+	// This flag should be adjusted before each Stop() or each BootGame() and similar because:
+	// 1. It forces an application to boot immediately by calling Run() in Load().
+	// 2. It signifies that we don't want to exit on Stop(), for example if we want to transition to another application.
 	bool m_force_boot = false;
+
 	bool m_has_gui = true;
 
 public:
diff --git a/rpcs3/rpcs3qt/main_window.cpp b/rpcs3/rpcs3qt/main_window.cpp
index 26f8a7a3f8..2c8a21e1d8 100644
--- a/rpcs3/rpcs3qt/main_window.cpp
+++ b/rpcs3/rpcs3qt/main_window.cpp
@@ -2227,7 +2227,10 @@ void main_window::closeEvent(QCloseEvent* closeEvent)
 	}
 
 	// Cleanly stop and quit the emulator.
-	Emu.Stop();
+	if (!Emu.IsStopped())
+	{
+		Emu.Stop();
+	}
 	Emu.Quit(true);
 }