diff --git a/GPU/Common/GPUStateUtils.cpp b/GPU/Common/GPUStateUtils.cpp
index 4cc1e9678f..09abb56ef9 100644
--- a/GPU/Common/GPUStateUtils.cpp
+++ b/GPU/Common/GPUStateUtils.cpp
@@ -515,6 +515,10 @@ float FromScaledDepth(float z) {
 	return (z - offset) * depthSliceFactor * 65535.0f;
 }
 
+float DepthSliceFactor() {
+	return depthSliceFactor;
+}
+
 void ConvertViewportAndScissor(bool useBufferedRendering, float renderWidth, float renderHeight, int bufferWidth, int bufferHeight, ViewportAndScissor &out) {
 	bool throughmode = gstate.isModeThrough();
 	out.dirtyProj = false;
diff --git a/GPU/Common/GPUStateUtils.h b/GPU/Common/GPUStateUtils.h
index 210573164b..0dba63b361 100644
--- a/GPU/Common/GPUStateUtils.h
+++ b/GPU/Common/GPUStateUtils.h
@@ -68,6 +68,7 @@ struct ViewportAndScissor {
 void ConvertViewportAndScissor(bool useBufferedRendering, float renderWidth, float renderHeight, int bufferWidth, int bufferHeight, ViewportAndScissor &out);
 float ToScaledDepth(u16 z);
 float FromScaledDepth(float z);
+float DepthSliceFactor();
 
 // These are common to all modern APIs and can be easily converted with a lookup table.
 enum class BlendFactor : uint8_t {
diff --git a/GPU/GLES/FragmentShaderGenerator.cpp b/GPU/GLES/FragmentShaderGenerator.cpp
index 9da24000df..911a4d6c4e 100644
--- a/GPU/GLES/FragmentShaderGenerator.cpp
+++ b/GPU/GLES/FragmentShaderGenerator.cpp
@@ -676,8 +676,16 @@ bool GenerateFragmentShader(const ShaderID &id, char *buffer) {
 #endif
 
 	if (gstate_c.Supports(GPU_ROUND_FRAGMENT_DEPTH_TO_16BIT)) {
+		const double scale = DepthSliceFactor() * 65535.0;
+
 		WRITE(p, "  highp float z = gl_FragCoord.z;\n");
-		WRITE(p, "  z = (1.0/65535.0) * floor(z * 65535.0);\n");
+		// We center the depth with an offset, but only its fraction matters.
+		// When (DepthSliceFactor() - 1) is odd, it will be 0.5, otherwise 0.
+		if (((int)(DepthSliceFactor() - 1.0f) & 1) == 1) {
+			WRITE(p, "  z = (floor((z * %f) - (1.0 / 2.0)) + (1.0 / 2.0)) * (1.0 / %f);\n", scale, scale);
+		} else {
+			WRITE(p, "  z = floor(z * %f) * (1.0 / %f);\n", scale, scale);
+		}
 		WRITE(p, "  gl_FragDepth = z;\n");
 	}