diff --git a/Source/Core/VideoCommon/Src/PixelShaderGen.cpp b/Source/Core/VideoCommon/Src/PixelShaderGen.cpp
index 7de5d12638..b4ad513d37 100644
--- a/Source/Core/VideoCommon/Src/PixelShaderGen.cpp
+++ b/Source/Core/VideoCommon/Src/PixelShaderGen.cpp
@@ -627,7 +627,10 @@ static inline void GeneratePixelShader(T& out, DSTALPHA_MODE dstAlphaMode, API_T
 
 	AlphaTest::TEST_RESULT Pretest = bpmem.alpha_test.TestResult();
 	uid_data.Pretest = Pretest;
-	if (Pretest == AlphaTest::UNDETERMINED)
+
+	// NOTE: Fragment may not be discarded if alpha test always fails and early depth test is enabled 
+	// (in this case we need to write a depth value if depth test passes regardless of the alpha testing result)
+	if (Pretest == AlphaTest::UNDETERMINED || (Pretest == AlphaTest::FAIL && bpmem.UseLateDepthTest()))
 		WriteAlphaTest<T>(out, uid_data, ApiType, dstAlphaMode, per_pixel_depth);