diff --git a/Common/System/System.h b/Common/System/System.h
index deebbac2d5..dbb10375d4 100644
--- a/Common/System/System.h
+++ b/Common/System/System.h
@@ -250,6 +250,7 @@ enum SystemProperty {
 	SYSPROP_INSTALLER_NAME,  // Useful on Android to check if we were installed from the play store.
 };
 
+// NOTE: Unlike requests or UIMessage, these are synchronous!
 enum class SystemNotification {
 	UI,
 	MEM_VIEW,
@@ -273,6 +274,8 @@ enum class SystemNotification {
 	AUDIO_MODE_CHANGED,
 	APP_SWITCH_MODE_CHANGED,
 	PAD_STATE_CHANGED,
+	CONFIG_LOADED,
+	BEFORE_CONFIG_SAVE_ON_EXIT,
 };
 
 // I guess it's not super great architecturally to centralize this, since it's not general - but same with a lot of
diff --git a/UI/NativeApp.cpp b/UI/NativeApp.cpp
index 81857bfae1..eafea2dfe7 100644
--- a/UI/NativeApp.cpp
+++ b/UI/NativeApp.cpp
@@ -575,6 +575,7 @@ void NativeInit(int argc, const char *argv[], const char *savegame_dir, const ch
 	// Note that if we don't have storage permission here, loading the config will
 	// fail and it will be set to the default. Later, we load again when we get permission.
 	g_Config.Load();
+	System_Notify(SystemNotification::CONFIG_LOADED);
 #endif
 
 	const char *fileToLog = nullptr;
@@ -1708,6 +1709,8 @@ void NativeShutdown() {
 		g_screenManager = nullptr;
 	}
 
+	System_Notify(SystemNotification::BEFORE_CONFIG_SAVE_ON_EXIT);
+
 	g_Config.Save("NativeShutdown");
 
 	g_i18nrepo.LogMissingKeys();
diff --git a/Windows/EmuThread.cpp b/Windows/EmuThread.cpp
index fbd86c37a5..5e6fe75e77 100644
--- a/Windows/EmuThread.cpp
+++ b/Windows/EmuThread.cpp
@@ -54,9 +54,6 @@ static GraphicsContext *g_graphicsContext;
 
 void MainThreadFunc();
 
-// On most other platforms, we let the "main" thread become the render thread and
-// start a separate emu thread from that, if needed. Should probably switch to that
-// to make it the same on all platforms.
 void MainThread_Start(bool separateEmuThread) {
 	useEmuThread = separateEmuThread;
 	mainThread = std::thread(&MainThreadFunc);
@@ -152,11 +149,6 @@ void MainThreadFunc() {
 	// We'll start up a separate thread we'll call Emu
 	SetCurrentThreadName(useEmuThread ? "RenderThread" : "EmuThread");
 
-	const HWND console = GetConsoleWindow();
-	if (console && g_Config.iConsoleWindowX != -1 && g_Config.iConsoleWindowY != -1) {
-		SetWindowPos(console, NULL, g_Config.iConsoleWindowX, g_Config.iConsoleWindowY, 0, 0, SWP_NOSIZE | SWP_NOZORDER);
-	}
-
 	System_SetWindowTitle("");
 
 	// We convert command line arguments to UTF-8 immediately.
@@ -319,12 +311,6 @@ void MainThreadFunc() {
 	delete g_graphicsContext;
 	g_graphicsContext = nullptr;
 
-	RECT rc;
-	if (console && GetWindowRect(console, &rc) && !IsIconic(console)) {
-		g_Config.iConsoleWindowX = rc.left;
-		g_Config.iConsoleWindowY = rc.top;
-	}
-
 	NativeShutdown();
 
 	PostMessage(MainWindow::GetHWND(), MainWindow::WM_USER_UPDATE_UI, 0, 0);
diff --git a/Windows/main.cpp b/Windows/main.cpp
index 5d7ea4bf0d..e0ddc78c50 100644
--- a/Windows/main.cpp
+++ b/Windows/main.cpp
@@ -594,6 +594,21 @@ void System_Notify(SystemNotification notification) {
 	case SystemNotification::APP_SWITCH_MODE_CHANGED:
 	case SystemNotification::UI_STATE_CHANGED:
 		break;
+	case SystemNotification::CONFIG_LOADED:
+	{
+		// This is too early to move the console into position - hasn't been allocated yet.
+		break;
+	}
+	case SystemNotification::BEFORE_CONFIG_SAVE_ON_EXIT:
+	{
+		RECT rc{};
+		const HWND console = GetConsoleWindow();
+		if (console && GetWindowRect(console, &rc) && !IsIconic(console)) {
+			g_Config.iConsoleWindowX = rc.left;
+			g_Config.iConsoleWindowY = rc.top;
+		}
+		break;
+	}
 	}
 }
 
@@ -1088,6 +1103,7 @@ int WINAPI WinMain(HINSTANCE _hInstance, HINSTANCE hPrevInstance, LPSTR szCmdLin
 	// if it's not loaded here first.
 	g_Config.SetSearchPath(GetSysDirectory(DIRECTORY_SYSTEM));
 	g_Config.Load(configFilename.c_str(), controlsConfigFilename.c_str());
+	System_Notify(SystemNotification::CONFIG_LOADED);
 
 	bool debugLogLevel = false;
 
@@ -1170,6 +1186,12 @@ int WINAPI WinMain(HINSTANCE _hInstance, HINSTANCE hPrevInstance, LPSTR szCmdLin
 	//   - It should be possible to log to a file without showing the console.
 	g_logManager.GetConsoleListener()->Init(showLog, 150, 120);
 
+	// Move the console into position.
+	const HWND console = GetConsoleWindow();
+	if (console && g_Config.iConsoleWindowX != -1 && g_Config.iConsoleWindowY != -1) {
+		SetWindowPos(console, NULL, g_Config.iConsoleWindowX, g_Config.iConsoleWindowY, 0, 0, SWP_NOSIZE | SWP_NOZORDER);
+	}
+
 	if (debugLogLevel) {
 		g_logManager.SetAllLogLevels(LogLevel::LDEBUG);
 	}