diff --git a/Source/Core/DolphinWX/Frame.cpp b/Source/Core/DolphinWX/Frame.cpp
index 25a09d13e1..d849324a9f 100644
--- a/Source/Core/DolphinWX/Frame.cpp
+++ b/Source/Core/DolphinWX/Frame.cpp
@@ -316,7 +316,7 @@ CFrame::CFrame(wxFrame* parent,
 	, m_LogWindow(nullptr), m_LogConfigWindow(nullptr)
 	, m_FifoPlayerDlg(nullptr), UseDebugger(_UseDebugger)
 	, m_bBatchMode(_BatchMode), m_bEdit(false), m_bTabSplit(false), m_bNoDocking(false)
-	, m_bGameLoading(false), m_bClosing(false)
+	, m_bGameLoading(false), m_bClosing(false), m_confirmStop(false)
 {
 	for (int i = 0; i <= IDM_CODEWINDOW - IDM_LOGWINDOW; i++)
 		bFloatWindow[i] = false;
@@ -643,6 +643,8 @@ void CFrame::OnHostMessage(wxCommandEvent& event)
 	case IDM_FULLSCREENREQUEST:
 		if (m_RenderFrame != nullptr)
 			m_RenderFrame->ShowFullScreen(event.GetInt() == 0 ? false : true);
+		if (m_confirmStop)
+			Core::SetState(Core::CORE_PAUSE);
 		break;
 
 	case WM_USER_CREATE:
@@ -1194,9 +1196,8 @@ void CFrame::DoFullscreen(bool bF)
 	{
 		m_RenderFrame->ShowFullScreen(true, wxFULLSCREEN_ALL);
 	}
-	else if (!g_ActiveConfig.backend_info.bSupportsExclusiveFullscreen ||
-		SConfig::GetInstance().m_LocalCoreStartupParameter.bRenderToMain ||
-		g_ActiveConfig.bForceBorderlessFullscreen)
+	else if (!g_Config.ExclusiveFullscreenEnabled() ||
+		SConfig::GetInstance().m_LocalCoreStartupParameter.bRenderToMain)
 	{
 		// Exiting exclusive fullscreen should be done from a Renderer callback.
 		// Therefore we don't exit fullscreen from here if we support exclusive mode.
diff --git a/Source/Core/DolphinWX/Frame.h b/Source/Core/DolphinWX/Frame.h
index 3ae9216c11..cbf9209d65 100644
--- a/Source/Core/DolphinWX/Frame.h
+++ b/Source/Core/DolphinWX/Frame.h
@@ -170,6 +170,7 @@ private:
 	bool m_bNoDocking;
 	bool m_bGameLoading;
 	bool m_bClosing;
+	bool m_confirmStop;
 
 	std::vector<std::string> drives;
 
diff --git a/Source/Core/DolphinWX/FrameTools.cpp b/Source/Core/DolphinWX/FrameTools.cpp
index 1885ddb55e..937809e050 100644
--- a/Source/Core/DolphinWX/FrameTools.cpp
+++ b/Source/Core/DolphinWX/FrameTools.cpp
@@ -95,6 +95,7 @@ Core::GetWindowHandle().
 #include "InputCommon/ControllerInterface/ControllerInterface.h"
 
 #include "VideoCommon/VideoBackendBase.h"
+#include "VideoCommon/VideoConfig.h"
 
 #ifdef _WIN32
 #ifndef SM_XVIRTUALSCREEN
@@ -119,8 +120,6 @@ extern "C" {
 class InputPlugin;
 class wxFrame;
 
-static bool confirmStop = false;
-
 // Create menu items
 // ---------------------
 void CFrame::CreateMenu()
@@ -1082,11 +1081,11 @@ void CFrame::DoStop()
 {
 	if (!Core::IsRunningAndStarted())
 		return;
-	if (confirmStop)
+	if (m_confirmStop)
 		return;
 
 	// don't let this function run again until it finishes, or is aborted.
-	confirmStop = true;
+	m_confirmStop = true;
 
 	m_bGameLoading = false;
 	if (Core::GetState() != Core::CORE_UNINITIALIZED ||
@@ -1100,8 +1099,21 @@ void CFrame::DoStop()
 		// Ask for confirmation in case the user accidentally clicked Stop / Escape
 		if (SConfig::GetInstance().m_LocalCoreStartupParameter.bConfirmStop)
 		{
+			// Pause the state during confirmation and restore it afterwards
 			Core::EState state = Core::GetState();
-			Core::SetState(Core::CORE_PAUSE);
+
+			// If exclusive fullscreen is not enabled then we can pause the emulation
+			// before we've exited fullscreen. If not then we need to exit fullscreen first.
+			if (!RendererIsFullscreen() || !g_Config.ExclusiveFullscreenEnabled() ||
+				SConfig::GetInstance().m_LocalCoreStartupParameter.bRenderToMain)
+			{
+				Core::SetState(Core::CORE_PAUSE);
+			}
+			else
+			{
+				DoFullscreen(false);
+			}
+
 			wxMessageDialog m_StopDlg(
 				this,
 				_("Do you want to stop the current emulation?"),
@@ -1113,7 +1125,7 @@ void CFrame::DoStop()
 			if (Ret != wxID_YES)
 			{
 				Core::SetState(state);
-				confirmStop = false;
+				m_confirmStop = false;
 				return;
 			}
 		}
@@ -1135,7 +1147,7 @@ void CFrame::OnStopped()
 {
 	wxEndBusyCursor();
 
-	confirmStop = false;
+	m_confirmStop = false;
 
 #if defined(HAVE_X11) && HAVE_X11
 	if (SConfig::GetInstance().m_LocalCoreStartupParameter.bDisableScreenSaver)
diff --git a/Source/Core/VideoBackends/D3D/Render.cpp b/Source/Core/VideoBackends/D3D/Render.cpp
index ae23516d5c..40b316787f 100644
--- a/Source/Core/VideoBackends/D3D/Render.cpp
+++ b/Source/Core/VideoBackends/D3D/Render.cpp
@@ -946,10 +946,10 @@ void Renderer::SwapImpl(u32 xfbAddr, u32 fbWidth, u32 fbHeight,const EFBRectangl
 	BOOL fullscreen_state;
 	if (SUCCEEDED(D3D::swapchain->GetFullscreenState(&fullscreen_state, nullptr)))
 	{
-		if (!!fullscreen_state != fullscreen)
+		if (!!fullscreen_state != fullscreen && Host_RendererHasFocus())
 		{
 			// We should be in fullscreen, but we're not. Restore it when we regain focus.
-			fullscreen_changed = Host_RendererHasFocus();
+			fullscreen_changed = true;
 		}
 	}
 
diff --git a/Source/Core/VideoCommon/VideoConfig.h b/Source/Core/VideoCommon/VideoConfig.h
index d2c5f1eaae..34d4f314c5 100644
--- a/Source/Core/VideoCommon/VideoConfig.h
+++ b/Source/Core/VideoCommon/VideoConfig.h
@@ -154,6 +154,7 @@ struct VideoConfig final
 	bool VirtualXFBEnabled() const { return bUseXFB && !bUseRealXFB; }
 	bool EFBCopiesToTextureEnabled() const { return bEFBCopyEnable && bCopyEFBToTexture; }
 	bool EFBCopiesToRamEnabled() const { return bEFBCopyEnable && !bCopyEFBToTexture; }
+	bool ExclusiveFullscreenEnabled() const { return backend_info.bSupportsExclusiveFullscreen && !bForceBorderlessFullscreen; }
 };
 
 extern VideoConfig g_Config;