diff --git a/GPU/GLES/FragmentShaderGenerator.cpp b/GPU/GLES/FragmentShaderGenerator.cpp
index 5d02b0ca796a..c31683f53c38 100644
--- a/GPU/GLES/FragmentShaderGenerator.cpp
+++ b/GPU/GLES/FragmentShaderGenerator.cpp
@@ -292,6 +292,7 @@ void ComputeFragmentShaderID(FragmentShaderID *id) {
 		bool enableAlphaDoubling = !alphaToColorDoubling && CanDoubleSrcBlendMode();
 		bool doTextureProjection = gstate.getUVGenMode() == GE_TEXMAP_TEXTURE_MATRIX;
 		bool doTextureAlpha = gstate.isTextureAlphaUsed();
+		bool computeAbsdiff = gstate.getBlendEq() == GE_BLENDMODE_ABSDIFF;
 		ReplaceAlphaType stencilToAlpha = ReplaceAlphaWithStencil();
 
 		// All texfuncs except replace are the same for RGB as for RGBA with full alpha.
@@ -326,11 +327,16 @@ void ComputeFragmentShaderID(FragmentShaderID *id) {
 			// 3 bits
 			id0 |= ReplaceAlphaWithStencilType() << 21;
 		}
+
 		id0 |= (alphaTestAgainstZero & 1) << 24;
 		if (enableAlphaTest)
 			gpuStats.numAlphaTestedDraws++;
 		else
 			gpuStats.numNonAlphaTestedDraws++;
+
+		if (computeAbsdiff) {
+			id0 |= (computeAbsdiff & 1) << 25;
+		}
 	}
 
 	id->d[0] = id0;
@@ -407,6 +413,7 @@ void GenerateFragmentShader(char *buffer) {
 	bool enableAlphaDoubling = !alphaToColorDoubling && CanDoubleSrcBlendMode();
 	bool doTextureProjection = gstate.getUVGenMode() == GE_TEXMAP_TEXTURE_MATRIX;
 	bool doTextureAlpha = gstate.isTextureAlphaUsed();
+	bool computeAbsdiff = gstate.getBlendEq() == GE_BLENDMODE_ABSDIFF;
 	ReplaceAlphaType stencilToAlpha = ReplaceAlphaWithStencil();
 
 	if (gstate_c.textureFullAlpha && gstate.getTextureFunction() != GE_TEXFUNC_REPLACE)
@@ -592,6 +599,11 @@ void GenerateFragmentShader(char *buffer) {
 		}
 	}
 
+	// Handle ABSDIFF blending mode using GL_EXT_shader_framebuffer_fetch
+	if (computeAbsdiff && gl_extensions.EXT_shader_framebuffer_fetch) {
+		WRITE(p, "  gl_FragColor.rgb = abs(v.rgb - gl_LastFragData[0].rgb);\n");
+	}
+
 	switch (stencilToAlpha) {
 	case REPLACE_ALPHA_DUALSOURCE:
 		WRITE(p, "  fragColor0 = vec4(v.rgb, 0.0);\n");
diff --git a/GPU/GLES/StateMapping.cpp b/GPU/GLES/StateMapping.cpp
index 1378d7efb52c..179039094f67 100644
--- a/GPU/GLES/StateMapping.cpp
+++ b/GPU/GLES/StateMapping.cpp
@@ -325,7 +325,12 @@ void TransformDrawEngine::ApplyDrawState(int prim) {
 		}
 
 		if (((blendFuncEq >= GE_BLENDMODE_MIN) && gl_extensions.EXT_blend_minmax) || gl_extensions.GLES3) {
-			glstate.blendEquation.set(eqLookup[blendFuncEq]);
+			if (blendFuncEq == GE_BLENDMODE_ABSDIFF && gl_extensions.EXT_shader_framebuffer_fetch) {
+				// Handle GE_BLENDMODE_ABSDIFF in fragment shader and turn off regular alpha blending here.
+				glstate.blend.set(false);
+			} else {
+				glstate.blendEquation.set(eqLookup[blendFuncEq]);
+			}
 		} else {
 			glstate.blendEquation.set(eqLookupNoMinMax[blendFuncEq]);
 		}