diff --git a/GPU/GLES/FragmentShaderGenerator.cpp b/GPU/GLES/FragmentShaderGenerator.cpp
index 78d56e7e2..80135e5c9 100644
--- a/GPU/GLES/FragmentShaderGenerator.cpp
+++ b/GPU/GLES/FragmentShaderGenerator.cpp
@@ -370,10 +370,9 @@ void ComputeFragmentShaderID(FragmentShaderID *id) {
 			id0 |= 1 << 1;
 			id0 |= gstate.getTextureFunction() << 2;
 			id0 |= (doTextureAlpha & 1) << 5; // rgb or rgba
+			id0 |= (gstate_c.flipTexture & 1) << 6;
 		}
 
-		// 6 is free.
-
 		id0 |= (lmode & 1) << 7;
 		if (enableAlphaTest) {
 			id0 |= 1 << 8;
@@ -585,10 +584,13 @@ void GenerateFragmentShader(char *buffer) {
 				// We may also be wrapping in such a surface, or either one in a too-small surface.
 				// Obviously, clamping to a smaller surface won't work.  But better to clamp to something.
 				std::string ucoord = "v_texcoord.x";
-				std::string vcoord = "1.0 - v_texcoord.y";
+				std::string vcoord = "v_texcoord.y";
 				if (doTextureProjection) {
 					ucoord += " / v_texcoord.z";
-					vcoord = "1.0 - (v_texcoord.y / v_texcoord.z)";
+					vcoord = "(v_texcoord.y / v_texcoord.z)";
+					// Vertex texcoords are NOT flipped when projecting despite gstate_c.flipTexture.
+				} else if (gstate_c.flipTexture) {
+					vcoord = "1.0 - " + vcoord;
 				}
 
 				if (gstate.isTexCoordClampedS()) {
@@ -603,10 +605,19 @@ void GenerateFragmentShader(char *buffer) {
 					vcoord = "mod(" + vcoord + ", u_texclamp.y)";
 				}
 
-				WRITE(p, "  vec2 fixedcoord = vec2(%s, 1.0 - %s);\n", ucoord.c_str(), vcoord.c_str());
+				if (gstate_c.flipTexture) {
+					vcoord = "1.0 - " + vcoord;
+				}
+
+				WRITE(p, "  vec2 fixedcoord = vec2(%s, %s);\n", ucoord.c_str(), vcoord.c_str());
 				texcoord = "fixedcoord";
 				// We already projected it.
 				doTextureProjection = false;
+			} else if (doTextureProjection && gstate_c.flipTexture) {
+				// Since we need to flip v, we project manually.
+				WRITE(p, "  vec2 fixedcoord = vec2(v_texcoord.x / v_texcoord.z, 1.0 - (v_texcoord.y / v_texcoord.z));\n");
+				texcoord = "fixedcoord";
+				doTextureProjection = false;
 			}
 
 			if (doTextureProjection) {
diff --git a/GPU/GLES/SoftwareTransform.cpp b/GPU/GLES/SoftwareTransform.cpp
index 54833007d..cf5e3d699 100644
--- a/GPU/GLES/SoftwareTransform.cpp
+++ b/GPU/GLES/SoftwareTransform.cpp
@@ -172,6 +172,8 @@ void TransformDrawEngine::SoftwareTransformAndDraw(
 	}
 
 	VertexReader reader(decoded, decVtxFormat, vertType);
+	// We flip in the fragment shader for GE_TEXMAP_TEXTURE_MATRIX.
+	const bool flipV = gstate_c.flipTexture && gstate.getUVGenMode() != GE_TEXMAP_TEXTURE_MATRIX;
 	for (int index = 0; index < maxIndex; index++) {
 		reader.Goto(index);
 
@@ -371,7 +373,7 @@ void TransformDrawEngine::SoftwareTransformAndDraw(
 		memcpy(&transformed[index].x, v, 3 * sizeof(float));
 		transformed[index].fog = fogCoef;
 		memcpy(&transformed[index].u, uv, 3 * sizeof(float));
-		if (gstate_c.flipTexture) {
+		if (flipV) {
 			transformed[index].v = 1.0f - transformed[index].v;
 		}
 		transformed[index].color0_32 = c0.ToRGBA();
diff --git a/GPU/GLES/VertexShaderGenerator.cpp b/GPU/GLES/VertexShaderGenerator.cpp
index 0a7c881da..768e6b17a 100644
--- a/GPU/GLES/VertexShaderGenerator.cpp
+++ b/GPU/GLES/VertexShaderGenerator.cpp
@@ -661,7 +661,8 @@ void GenerateVertexShader(int prim, u32 vertType, char *buffer, bool useHWTransf
 				break;
 			}
 
-			if (flipV)
+			// Will flip in the fragment for GE_TEXMAP_TEXTURE_MATRIX.
+			if (flipV && gstate.getUVGenMode() != GE_TEXMAP_TEXTURE_MATRIX)
 				WRITE(p, "  v_texcoord.y = 1.0 - v_texcoord.y;\n");
 		}