diff --git a/Source/Core/DolphinWX/GLInterface/X11_Util.cpp b/Source/Core/DolphinWX/GLInterface/X11_Util.cpp
index 610fd67949..79d0d76b8b 100644
--- a/Source/Core/DolphinWX/GLInterface/X11_Util.cpp
+++ b/Source/Core/DolphinWX/GLInterface/X11_Util.cpp
@@ -8,8 +8,6 @@
 
 void cX11Window::CreateXWindow(void)
 {
-	Atom wmProtocols[1];
-
 	// Setup window attributes
 	GLWin.attr.colormap = XCreateColormap(GLWin.dpy,
 			GLWin.parent, GLWin.vi->visual, AllocNone);
@@ -22,9 +20,7 @@ void cX11Window::CreateXWindow(void)
 			0, 0, 1, 1, 0,
 			GLWin.vi->depth, InputOutput, GLWin.vi->visual,
 			CWBorderPixel | CWBackPixel | CWColormap | CWEventMask, &GLWin.attr);
-	wmProtocols[0] = XInternAtom(GLWin.dpy, "WM_DELETE_WINDOW", True);
-	XSetWMProtocols(GLWin.dpy, GLWin.win, wmProtocols, 1);
-	XMapRaised(GLWin.dpy, GLWin.win);
+	XMapWindow(GLWin.dpy, GLWin.win);
 	XSync(GLWin.dpy, True);
 
 	GLWin.xEventThread = std::thread(&cX11Window::XEventThread, this);
@@ -51,11 +47,6 @@ void cX11Window::XEventThread()
 				case ConfigureNotify:
 					GLInterface->SetBackBufferDimensions(event.xconfigure.width, event.xconfigure.height);
 					break;
-				case ClientMessage:
-					if ((unsigned long) event.xclient.data.l[0] ==
-							XInternAtom(GLWin.dpy, "WM_DELETE_WINDOW", False))
-						Host_Message(WM_USER_STOP);
-					break;
 				default:
 					break;
 			}
diff --git a/Source/Core/DolphinWX/MainNoGUI.cpp b/Source/Core/DolphinWX/MainNoGUI.cpp
index 74e9cc00a0..9231b3ef3a 100644
--- a/Source/Core/DolphinWX/MainNoGUI.cpp
+++ b/Source/Core/DolphinWX/MainNoGUI.cpp
@@ -148,6 +148,9 @@ class PlatformX11 : public Platform
 					  SConfig::GetInstance().m_LocalCoreStartupParameter.iRenderWindowHeight,
 					  0, 0, BlackPixel(dpy, 0));
 		XSelectInput(dpy, win, KeyPressMask | FocusChangeMask);
+		Atom wmProtocols[1];
+		wmProtocols[0] = XInternAtom(dpy, "WM_DELETE_WINDOW", True);
+		XSetWMProtocols(dpy, win, wmProtocols, 1);
 		XMapRaised(dpy, win);
 		XFlush(dpy);
 		windowHandle = (void *) win;
@@ -250,6 +253,10 @@ class PlatformX11 : public Platform
 					if (SConfig::GetInstance().m_LocalCoreStartupParameter.bHideCursor)
 						XUndefineCursor(dpy, win);
 					break;
+				case ClientMessage:
+					if ((unsigned long) event.xclient.data.l[0] == XInternAtom(dpy, "WM_DELETE_WINDOW", False))
+						running = false;
+					break;
 				}
 			}
 			if (!fullscreen)