diff --git a/GPU/Common/GPUStateUtils.cpp b/GPU/Common/GPUStateUtils.cpp
index 824d3827b1..2e952270c3 100644
--- a/GPU/Common/GPUStateUtils.cpp
+++ b/GPU/Common/GPUStateUtils.cpp
@@ -813,22 +813,16 @@ static inline bool blendColorSimilar(uint32_t a, uint32_t b, int margin = 25) {
 }
 
 // Try to simulate some common logic ops.
-void ApplyStencilReplaceAndLogicOp(ReplaceAlphaType replaceAlphaWithStencil, GenericBlendState &blendState) {
-	StencilValueType stencilType = STENCIL_VALUE_KEEP;
-	if (replaceAlphaWithStencil == REPLACE_ALPHA_YES) {
-		stencilType = ReplaceAlphaWithStencilType();
-	}
-
-	// Normally, we would add src + 0, but the logic op may have us do differently.
-	BlendFactor srcBlend = BlendFactor::ONE;
-	BlendFactor dstBlend = BlendFactor::ZERO;
-	BlendEq blendEq = BlendEq::ADD;
-
+static void ApplyLogicOp(BlendFactor &srcBlend, BlendFactor &dstBlend, BlendEq &blendEq) {
+	// Note: our shader solution applies logic ops BEFORE blending, not correctly after.
+	// This is however fine for the most common ones, like CLEAR/NOOP/SET, etc.
 	if (!gstate_c.Supports(GPU_SUPPORTS_LOGIC_OP)) {
 		if (gstate.isLogicOpEnabled()) {
 			switch (gstate.getLogicOp()) {
 			case GE_LOGIC_CLEAR:
 				srcBlend = BlendFactor::ZERO;
+				dstBlend = BlendFactor::ZERO;
+				blendEq = BlendEq::ADD;
 				break;
 			case GE_LOGIC_AND:
 			case GE_LOGIC_AND_REVERSE:
@@ -856,6 +850,7 @@ void ApplyStencilReplaceAndLogicOp(ReplaceAlphaType replaceAlphaWithStencil, Gen
 			case GE_LOGIC_NOOP:
 				srcBlend = BlendFactor::ZERO;
 				dstBlend = BlendFactor::ONE;
+				blendEq = BlendEq::ADD;
 				break;
 			case GE_LOGIC_XOR:
 				WARN_LOG_REPORT_ONCE(d3dLogicOpOrXor, G3D, "Unsupported XOR logic op: %x", gstate.getLogicOp());
@@ -870,14 +865,30 @@ void ApplyStencilReplaceAndLogicOp(ReplaceAlphaType replaceAlphaWithStencil, Gen
 				WARN_LOG_REPORT_ONCE(d3dLogicOpOrReverse, G3D, "Unsupported OR REVERSE logic op: %x", gstate.getLogicOp());
 				break;
 			case GE_LOGIC_SET:
+				srcBlend = BlendFactor::ONE;
 				dstBlend = BlendFactor::ONE;
+				blendEq = BlendEq::ADD;
 				WARN_LOG_REPORT_ONCE(d3dLogicOpSet, G3D, "Attempted set for logic op: %x", gstate.getLogicOp());
 				break;
 			}
 		}
 	}
+}
 
-	// We're not blending, but we may still want to blend for stencil.
+// Try to simulate some common logic ops.
+void ApplyStencilReplaceAndLogicOp(ReplaceAlphaType replaceAlphaWithStencil, GenericBlendState &blendState) {
+	StencilValueType stencilType = STENCIL_VALUE_KEEP;
+	if (replaceAlphaWithStencil == REPLACE_ALPHA_YES) {
+		stencilType = ReplaceAlphaWithStencilType();
+	}
+
+	// Normally, we would add src + 0 with blending off, but the logic op may have us do differently.
+	BlendFactor srcBlend = BlendFactor::ONE;
+	BlendFactor dstBlend = BlendFactor::ZERO;
+	BlendEq blendEq = BlendEq::ADD;
+	ApplyLogicOp(srcBlend, dstBlend, blendEq);
+
+	// We're not blending, but we may still want to "blend" for stencil.
 	// This is only useful for INCR/DECR/INVERT.  Others can write directly.
 	switch (stencilType) {
 	case STENCIL_VALUE_INCR_4:
@@ -1105,6 +1116,15 @@ void ConvertBlendState(GenericBlendState &blendState, bool allowShaderBlend) {
 #endif
 
 	// At this point, through all paths above, glBlendFuncA and glBlendFuncB will be set right somehow.
+	BlendEq colorEq;
+	if (gstate_c.Supports(GPU_SUPPORTS_BLEND_MINMAX)) {
+		colorEq = eqLookup[blendFuncEq];
+	} else {
+		colorEq = eqLookupNoMinMax[blendFuncEq];
+	}
+
+	// Attempt to apply the logic op, if any.
+	ApplyLogicOp(glBlendFuncA, glBlendFuncB, colorEq);
 
 	// The stencil-to-alpha in fragment shader doesn't apply here (blending is enabled), and we shouldn't
 	// do any blending in the alpha channel as that doesn't seem to happen on PSP.  So, we attempt to
@@ -1174,11 +1194,7 @@ void ConvertBlendState(GenericBlendState &blendState, bool allowShaderBlend) {
 		blendState.setFactors(glBlendFuncA, glBlendFuncB, BlendFactor::ZERO, BlendFactor::ONE);
 	}
 
-	if (gstate_c.Supports(GPU_SUPPORTS_BLEND_MINMAX)) {
-		blendState.setEquation(eqLookup[blendFuncEq], alphaEq);
-	} else {
-		blendState.setEquation(eqLookupNoMinMax[blendFuncEq], alphaEq);
-	}
+	blendState.setEquation(colorEq, alphaEq);
 }
 
 static void ConvertStencilFunc5551(GenericStencilFuncState &state) {
diff --git a/GPU/Software/Rasterizer.cpp b/GPU/Software/Rasterizer.cpp
index f6b6e398e7..ebed8f36de 100644
--- a/GPU/Software/Rasterizer.cpp
+++ b/GPU/Software/Rasterizer.cpp
@@ -972,7 +972,7 @@ inline void DrawSinglePixel(const DrawingCoords &p, u16 z, u8 fog, const Vec4<in
 #endif
 	}
 
-	// TODO: Is alpha blending still performed if logic ops are enabled?
+	// Logic ops are applied after blending (if blending is enabled.)
 	if (gstate.isLogicOpEnabled() && !clearMode) {
 		// Logic ops don't affect stencil.
 		new_color = (stencil << 24) | (ApplyLogicOp(gstate.getLogicOp(), old_color, new_color) & 0x00FFFFFF);
@@ -980,9 +980,8 @@ inline void DrawSinglePixel(const DrawingCoords &p, u16 z, u8 fog, const Vec4<in
 
 	if (clearMode) {
 		new_color = (new_color & ~gstate.getClearModeColorMask()) | (old_color & gstate.getClearModeColorMask());
-	} else {
-		new_color = (new_color & ~gstate.getColorMask()) | (old_color & gstate.getColorMask());
 	}
+	new_color = (new_color & ~gstate.getColorMask()) | (old_color & gstate.getColorMask());
 
 	// TODO: Dither before or inside SetPixelColor
 	SetPixelColor(p.x, p.y, new_color);
@@ -1554,6 +1553,9 @@ void ClearRectangle(const VertexData &v0, const VertexData &v1)
 		break;
 	}
 
+	// The pixel write masks are respected in clear mode.
+	keepOldMask &= ~gstate.getColorMask();
+
 	if (keepOldMask == 0) {
 		ScreenCoords pprime(minX, minY, 0);
 		const int stride = gstate.FrameBufStride();
diff --git a/headless/SDLHeadlessHost.h b/headless/SDLHeadlessHost.h
index daa0fe0413..3907f3ab5e 100644
--- a/headless/SDLHeadlessHost.h
+++ b/headless/SDLHeadlessHost.h
@@ -49,7 +49,6 @@ protected:
 		STOPPED,
 	};
 
-	GraphicsContext *gfx_;
 	volatile RenderThreadState threadState_ = RenderThreadState::IDLE;
 };
 
diff --git a/headless/WindowsHeadlessHost.h b/headless/WindowsHeadlessHost.h
index 853eee1eb5..907b20cdf6 100644
--- a/headless/WindowsHeadlessHost.h
+++ b/headless/WindowsHeadlessHost.h
@@ -53,6 +53,5 @@ protected:
 	HWND hWnd;
 	HDC hDC;
 	HGLRC hRC;
-	GraphicsContext *gfx_;
 	volatile RenderThreadState threadState_ = RenderThreadState::IDLE;
 };