diff --git a/Ryujinx.Graphics.Gpu/Shader/DiskCache/DiskCacheHostStorage.cs b/Ryujinx.Graphics.Gpu/Shader/DiskCache/DiskCacheHostStorage.cs
index 2168c18591..86d453cc78 100644
--- a/Ryujinx.Graphics.Gpu/Shader/DiskCache/DiskCacheHostStorage.cs
+++ b/Ryujinx.Graphics.Gpu/Shader/DiskCache/DiskCacheHostStorage.cs
@@ -22,7 +22,7 @@ namespace Ryujinx.Graphics.Gpu.Shader.DiskCache
         private const ushort FileFormatVersionMajor = 1;
         private const ushort FileFormatVersionMinor = 2;
         private const uint FileFormatVersionPacked = ((uint)FileFormatVersionMajor << 16) | FileFormatVersionMinor;
-        private const uint CodeGenVersion = 3759;
+        private const uint CodeGenVersion = 3781;
 
         private const string SharedTocFileName = "shared.toc";
         private const string SharedDataFileName = "shared.data";
diff --git a/Ryujinx.Graphics.Shader/Translation/ShaderConfig.cs b/Ryujinx.Graphics.Shader/Translation/ShaderConfig.cs
index b18979d8fa..2274716018 100644
--- a/Ryujinx.Graphics.Shader/Translation/ShaderConfig.cs
+++ b/Ryujinx.Graphics.Shader/Translation/ShaderConfig.cs
@@ -306,7 +306,10 @@ namespace Ryujinx.Graphics.Shader.Translation
                 config._perPatchAttributeLocations = locationsMap;
             }
 
-            if (config.Stage != ShaderStage.Fragment)
+            // We don't consider geometry shaders using the geometry shader passthrough feature
+            // as being the last because when this feature is used, it can't actually modify any of the outputs,
+            // so the stage that comes before it is the last one that can do modifications.
+            if (config.Stage != ShaderStage.Fragment && (config.Stage != ShaderStage.Geometry || !config.GpPassthrough))
             {
                 LastInVertexPipeline = false;
             }