diff --git a/Source/Core/VideoCommon/GeometryShaderGen.cpp b/Source/Core/VideoCommon/GeometryShaderGen.cpp
index 997e809860..10895ccf88 100644
--- a/Source/Core/VideoCommon/GeometryShaderGen.cpp
+++ b/Source/Core/VideoCommon/GeometryShaderGen.cpp
@@ -123,9 +123,6 @@ ShaderCode GenerateGeometryShaderCode(APIType api_type, const ShaderHostConfig&
                             GetInterpolationQualifier(msaa, ssaa, true, false),
                             ShaderStage::Geometry);
 
-    if (stereo)
-      out.Write("\tflat int layer;\n");
-
     out.Write("}} ps;\n");
 
     out.Write("void main()\n{{\n");
@@ -136,7 +133,9 @@ ShaderCode GenerateGeometryShaderCode(APIType api_type, const ShaderHostConfig&
     out.Write("\tVS_OUTPUT o;\n");
 
     if (stereo)
+    {
       out.Write("\tuint layer : SV_RenderTargetArrayIndex;\n");
+    }
     out.Write("\tfloat4 posout : SV_Position;\n");
 
     out.Write("}};\n");
@@ -354,9 +353,12 @@ static void EmitVertex(ShaderCode& out, const ShaderHostConfig& host_config,
   if (stereo)
   {
     // Select the output layer
-    out.Write("\tps.layer = eye;\n");
     if (api_type == APIType::OpenGL || api_type == APIType::Vulkan)
       out.Write("\tgl_Layer = eye;\n");
+    else
+    {
+      out.Write("\tps.layer = eye;\n");
+    }
   }
 
   if (api_type == APIType::OpenGL || api_type == APIType::Vulkan)
diff --git a/Source/Core/VideoCommon/PixelShaderGen.cpp b/Source/Core/VideoCommon/PixelShaderGen.cpp
index 11ac3a0c1a..93452de011 100644
--- a/Source/Core/VideoCommon/PixelShaderGen.cpp
+++ b/Source/Core/VideoCommon/PixelShaderGen.cpp
@@ -909,9 +909,6 @@ ShaderCode GeneratePixelShaderCode(APIType api_type, const ShaderHostConfig& hos
     GenerateVSOutputMembers(out, api_type, uid_data->genMode_numtexgens, host_config,
                             GetInterpolationQualifier(msaa, ssaa, true, true), ShaderStage::Pixel);
 
-    if (stereo)
-      out.Write("\tflat int layer;\n");
-
     out.Write("}};\n");
   }
   else
@@ -967,8 +964,15 @@ ShaderCode GeneratePixelShaderCode(APIType api_type, const ShaderHostConfig& hos
   {
     out.Write("\tfloat4 ocol1;\n");
   }
-  if (!stereo)
+
+  if (host_config.backend_geometry_shaders && stereo)
+  {
+    out.Write("\tint layer = gl_Layer;\n");
+  }
+  else
+  {
     out.Write("\tint layer = 0;\n");
+  }
 
   out.Write("\tint4 c0 = " I_COLORS "[1], c1 = " I_COLORS "[2], c2 = " I_COLORS
             "[3], prev = " I_COLORS "[0];\n"
diff --git a/Source/Core/VideoCommon/UberShaderPixel.cpp b/Source/Core/VideoCommon/UberShaderPixel.cpp
index eff6bfae44..de1aaa72f7 100644
--- a/Source/Core/VideoCommon/UberShaderPixel.cpp
+++ b/Source/Core/VideoCommon/UberShaderPixel.cpp
@@ -128,9 +128,6 @@ ShaderCode GenPixelShader(APIType api_type, const ShaderHostConfig& host_config,
     GenerateVSOutputMembers(out, api_type, numTexgen, host_config,
                             GetInterpolationQualifier(msaa, ssaa, true, true), ShaderStage::Pixel);
 
-    if (stereo)
-      out.Write("  flat int layer;\n");
-
     out.Write("}};\n\n");
   }
   else
@@ -538,8 +535,15 @@ ShaderCode GenPixelShader(APIType api_type, const ShaderHostConfig& host_config,
   {
     out.Write("  float4 ocol1;\n");
   }
-  if (!stereo)
-    out.Write("  int layer = 0;\n");
+
+  if (host_config.backend_geometry_shaders && stereo)
+  {
+    out.Write("\tint layer = gl_Layer;\n");
+  }
+  else
+  {
+    out.Write("\tint layer = 0;\n");
+  }
 
   out.Write("  int3 tevcoord = int3(0, 0, 0);\n"
             "  State s;\n"