diff --git a/GPU/GLES/FragmentShaderGenerator.cpp b/GPU/GLES/FragmentShaderGenerator.cpp
index 799f645010..04dd419960 100644
--- a/GPU/GLES/FragmentShaderGenerator.cpp
+++ b/GPU/GLES/FragmentShaderGenerator.cpp
@@ -99,6 +99,44 @@ static bool IsAlphaTestTriviallyTrue() {
 	}
 }
 
+const bool nonAlphaSrcFactors[16] = {
+	true,  // GE_SRCBLEND_DSTCOLOR,
+	true,  // GE_SRCBLEND_INVDSTCOLOR,
+	false, // GE_SRCBLEND_SRCALPHA,
+	false, // GE_SRCBLEND_INVSRCALPHA,
+	true,  // GE_SRCBLEND_DSTALPHA,
+	true,  // GE_SRCBLEND_INVDSTALPHA,
+	false, // GE_SRCBLEND_DOUBLESRCALPHA,
+	false, // GE_SRCBLEND_DOUBLEINVSRCALPHA,
+	true,  // GE_SRCBLEND_DOUBLEDSTALPHA,
+	true,  // GE_SRCBLEND_DOUBLEINVDSTALPHA,
+	true,  // GE_SRCBLEND_FIXA,
+};
+
+const bool nonAlphaDestFactors[16] = {
+	true,  // GE_DSTBLEND_SRCCOLOR,
+	true,  // GE_DSTBLEND_INVSRCCOLOR,
+	false, // GE_DSTBLEND_SRCALPHA,
+	false, // GE_DSTBLEND_INVSRCALPHA,
+	true,  // GE_DSTBLEND_DSTALPHA,
+	true,  // GE_DSTBLEND_INVDSTALPHA,
+	false, // GE_DSTBLEND_DOUBLESRCALPHA,
+	false, // GE_DSTBLEND_DOUBLEINVSRCALPHA,
+	true,  // GE_DSTBLEND_DOUBLEDSTALPHA,
+	true,  // GE_DSTBLEND_DOUBLEINVDSTALPHA,
+	true,  // GE_DSTBLEND_FIXB,
+};
+
+bool CanReplaceAlphaWithStencil() {
+	if (!gstate.isStencilTestEnabled()) {
+		return false;
+	}
+	if (gstate.isAlphaBlendEnabled()) {
+		return nonAlphaSrcFactors[gstate.getBlendFuncA()] && nonAlphaDestFactors[gstate.getBlendFuncA()];
+	}
+	return true;
+}
+
 StencilValueType ReplaceAlphaWithStencilType() {
 	switch (gstate.FrameBufFormat()) {
 	case GE_FORMAT_565:
@@ -214,7 +252,7 @@ void ComputeFragmentShaderID(FragmentShaderID *id) {
 		bool enableAlphaDoubling = CanDoubleSrcBlendMode();
 		bool doTextureProjection = gstate.getUVGenMode() == GE_TEXMAP_TEXTURE_MATRIX;
 		bool doTextureAlpha = gstate.isTextureAlphaUsed();
-		bool stencilToAlpha = gstate.isStencilTestEnabled() && !gstate.isAlphaBlendEnabled();
+		bool stencilToAlpha = CanReplaceAlphaWithStencil();
 
 		// All texfuncs except replace are the same for RGB as for RGBA with full alpha.
 		if (gstate_c.textureFullAlpha && gstate.getTextureFunction() != GE_TEXFUNC_REPLACE)
@@ -284,7 +322,7 @@ void GenerateFragmentShader(char *buffer) {
 	bool enableAlphaDoubling = CanDoubleSrcBlendMode();
 	bool doTextureProjection = gstate.getUVGenMode() == GE_TEXMAP_TEXTURE_MATRIX;
 	bool doTextureAlpha = gstate.isTextureAlphaUsed();
-	bool stencilToAlpha = !gstate.isModeClear() && gstate.isStencilTestEnabled() && !gstate.isAlphaBlendEnabled();
+	bool stencilToAlpha = !gstate.isModeClear() && CanReplaceAlphaWithStencil();
 
 	if (gstate_c.textureFullAlpha && gstate.getTextureFunction() != GE_TEXFUNC_REPLACE)
 		doTextureAlpha = false;
diff --git a/GPU/GLES/FragmentShaderGenerator.h b/GPU/GLES/FragmentShaderGenerator.h
index f183dfc70b..e3e147f8e3 100644
--- a/GPU/GLES/FragmentShaderGenerator.h
+++ b/GPU/GLES/FragmentShaderGenerator.h
@@ -53,4 +53,5 @@ enum StencilValueType {
 };
 
 StencilValueType ReplaceAlphaWithStencilType();
+bool CanReplaceAlphaWithStencil();
 
diff --git a/GPU/GLES/StateMapping.cpp b/GPU/GLES/StateMapping.cpp
index 5060171f36..9942e6f55d 100644
--- a/GPU/GLES/StateMapping.cpp
+++ b/GPU/GLES/StateMapping.cpp
@@ -249,7 +249,10 @@ void TransformDrawEngine::ApplyDrawState(int prim) {
 		// do any blending in the alpha channel as that doesn't seem to happen on PSP. So lacking a better option,
 		// the only value we can set alpha to here without multipass and dual source alpha is zero (by setting
 		// the factors to zero). So let's do that.
-		if (gstate.isStencilTestEnabled()) {
+		if (CanReplaceAlphaWithStencil()) {
+			// Let the fragment shader take care of it.
+			glstate.blendFuncSeparate.set(glBlendFuncA, glBlendFuncB, GL_ONE, GL_ZERO);
+		} else if (gstate.isStencilTestEnabled()) {
 			switch (ReplaceAlphaWithStencilType()) {
 			case STENCIL_VALUE_KEEP:
 				glstate.blendFuncSeparate.set(glBlendFuncA, glBlendFuncB, GL_ZERO, GL_ONE);