diff --git a/Common/UI/Screen.cpp b/Common/UI/Screen.cpp
index 1bf1d32f95f4..bf626ce653bd 100644
--- a/Common/UI/Screen.cpp
+++ b/Common/UI/Screen.cpp
@@ -168,9 +168,10 @@ ScreenRenderFlags ScreenManager::render() {
 		auto iter = stack_.end();
 		Screen *coveringScreen = nullptr;
 		Screen *backgroundScreen = nullptr;
+		bool first = true;
 		do {
 			--iter;
-			if (!backgroundScreen && iter->screen->canBeBackground()) {
+			if (!backgroundScreen && iter->screen->canBeBackground(first)) {
 				// There still might be a screen that wants to be background - generally the EmuScreen if present.
 				layers.push_back(iter->screen);
 				backgroundScreen = iter->screen;
@@ -180,6 +181,7 @@ ScreenRenderFlags ScreenManager::render() {
 			if (iter->flags != LAYER_TRANSPARENT) {
 				coveringScreen = iter->screen;
 			}
+			first = false;
 		} while (iter != stack_.begin());
 
 		// Confusing-looking expression, argh! Note the '_'
@@ -189,7 +191,6 @@ ScreenRenderFlags ScreenManager::render() {
 		}
 
 		// OK, now we iterate backwards over our little pile of collected screens.
-		bool first = true;
 		for (int i = (int)layers.size() - 1; i >= 0; i--) {
 			ScreenRenderMode mode = ScreenRenderMode::DEFAULT;
 			if (i == (int)layers.size() - 1) {
diff --git a/Common/UI/Screen.h b/Common/UI/Screen.h
index e65b0d8d7993..e7232a84009e 100644
--- a/Common/UI/Screen.h
+++ b/Common/UI/Screen.h
@@ -76,7 +76,7 @@ class Screen {
 	virtual void sendMessage(UIMessage message, const char *value) {}
 	virtual void deviceLost() {}
 	virtual void deviceRestored() {}
-	virtual bool canBeBackground() const { return false; }
+	virtual bool canBeBackground(bool isTop) const { return false; }
 	virtual bool wantBrightBackground() const { return false; }  // special hack for DisplayLayoutScreen.
 
 	virtual void focusChanged(ScreenFocusChange focusChange);
diff --git a/UI/EmuScreen.cpp b/UI/EmuScreen.cpp
index 51f1fc47c44b..74d34a2c0c04 100644
--- a/UI/EmuScreen.cpp
+++ b/UI/EmuScreen.cpp
@@ -1415,9 +1415,10 @@ static void DrawFPS(UIContext *ctx, const Bounds &bounds) {
 	ctx->RebindTexture();
 }
 
-bool EmuScreen::canBeBackground() const {
-	if (g_Config.bSkipBufferEffects)
-		return false;
+bool EmuScreen::canBeBackground(bool isTop) const {
+	if (g_Config.bSkipBufferEffects) {
+		return isTop || (g_Config.bTransparentBackground && g_Config.bRunBehindPauseMenu);
+	}
 
 	bool forceTransparent = false;  // this needs to be true somehow on the display layout screen.
 
@@ -1446,6 +1447,8 @@ ScreenRenderFlags EmuScreen::render(ScreenRenderMode mode) {
 	if (!draw)
 		return flags;  // shouldn't really happen but I've seen a suspicious stack trace..
 
+	bool skipBufferEffects = g_Config.bSkipBufferEffects;
+
 	if (mode & ScreenRenderMode::FIRST) {
 		// Actually, always gonna be first when it exists (?)
 
@@ -1472,6 +1475,8 @@ ScreenRenderFlags EmuScreen::render(ScreenRenderMode mode) {
 			viewport.MaxDepth = 1.0;
 			viewport.MinDepth = 0.0;
 			draw->SetViewport(viewport);
+
+			skipBufferEffects = true;
 		}
 		draw->SetTargetSize(g_display.pixel_xres, g_display.pixel_yres);
 	}
@@ -1568,14 +1573,22 @@ ScreenRenderFlags EmuScreen::render(ScreenRenderMode mode) {
 		PSP_EndHostFrame();
 	}
 
-	if (gpu && !gpu->PresentedThisFrame()) {
+	if (gpu && !gpu->PresentedThisFrame() && !skipBufferEffects) {
 		draw->BindFramebufferAsRenderTarget(nullptr, { RPAction::CLEAR, RPAction::CLEAR, RPAction::CLEAR }, "EmuScreen_NoFrame");
+		Viewport viewport{ 0.0f, 0.0f, (float)g_display.pixel_xres, (float)g_display.pixel_yres, 0.0f, 1.0f };
+		draw->SetViewport(viewport);
+		draw->SetScissorRect(0, 0, g_display.pixel_xres, g_display.pixel_yres);
 	}
 
 	if (!(mode & ScreenRenderMode::TOP)) {
 		// We're in run-behind mode, but we don't want to draw chat, debug UI and stuff.
 		// So, darken and bail here.
-
+		if (skipBufferEffects) {
+			// Need to reset viewport/scissor.
+			Viewport viewport{ 0.0f, 0.0f, (float)g_display.pixel_xres, (float)g_display.pixel_yres, 0.0f, 1.0f };
+			draw->SetViewport(viewport);
+			draw->SetScissorRect(0, 0, g_display.pixel_xres, g_display.pixel_yres);
+		}
 		darken();
 		return flags;
 	}
diff --git a/UI/EmuScreen.h b/UI/EmuScreen.h
index a97273027450..bcf3171a3e48 100644
--- a/UI/EmuScreen.h
+++ b/UI/EmuScreen.h
@@ -46,7 +46,7 @@ class EmuScreen : public UIScreen {
 	void dialogFinished(const Screen *dialog, DialogResult result) override;
 	void sendMessage(UIMessage message, const char *value) override;
 	void resized() override;
-	bool canBeBackground() const override;
+	bool canBeBackground(bool isTop) const override;
 
 	// Note: Unlike your average boring UIScreen, here we override the Unsync* functions
 	// to get minimal latency and full control. We forward to UIScreen when needed.