diff --git a/Source/Core/VideoCommon/PixelShaderGen.cpp b/Source/Core/VideoCommon/PixelShaderGen.cpp
index aae881a0f1..e34251e110 100644
--- a/Source/Core/VideoCommon/PixelShaderGen.cpp
+++ b/Source/Core/VideoCommon/PixelShaderGen.cpp
@@ -338,7 +338,8 @@ PixelShaderUid GetPixelShaderUid()
   return out;
 }
 
-void ClearUnusedPixelShaderUidBits(APIType ApiType, PixelShaderUid* uid)
+void ClearUnusedPixelShaderUidBits(APIType ApiType, const ShaderHostConfig& host_config,
+                                   PixelShaderUid* uid)
 {
   pixel_shader_uid_data* uid_data = uid->GetUidData<pixel_shader_uid_data>();
 
diff --git a/Source/Core/VideoCommon/PixelShaderGen.h b/Source/Core/VideoCommon/PixelShaderGen.h
index 2e630e2e49..da5137b8cb 100644
--- a/Source/Core/VideoCommon/PixelShaderGen.h
+++ b/Source/Core/VideoCommon/PixelShaderGen.h
@@ -168,5 +168,6 @@ ShaderCode GeneratePixelShaderCode(APIType ApiType, const ShaderHostConfig& host
                                    const pixel_shader_uid_data* uid_data);
 void WritePixelShaderCommonHeader(ShaderCode& out, APIType ApiType, u32 num_texgens,
                                   bool per_pixel_lighting, bool bounding_box);
-void ClearUnusedPixelShaderUidBits(APIType ApiType, PixelShaderUid* uid);
+void ClearUnusedPixelShaderUidBits(APIType ApiType, const ShaderHostConfig& host_config,
+                                   PixelShaderUid* uid);
 PixelShaderUid GetPixelShaderUid();
diff --git a/Source/Core/VideoCommon/ShaderCache.cpp b/Source/Core/VideoCommon/ShaderCache.cpp
index 6ab6f17fa5..13b1bfc0fc 100644
--- a/Source/Core/VideoCommon/ShaderCache.cpp
+++ b/Source/Core/VideoCommon/ShaderCache.cpp
@@ -456,12 +456,15 @@ std::optional<AbstractPipelineConfig> ShaderCache::GetGXPipelineConfig(const GXP
   else
     vs = InsertVertexShader(config.vs_uid, CompileVertexShader(config.vs_uid));
 
+  PixelShaderUid ps_uid = config.ps_uid;
+  ClearUnusedPixelShaderUidBits(m_api_type, m_host_config, &ps_uid);
+
   const AbstractShader* ps;
-  auto ps_iter = m_ps_cache.shader_map.find(config.ps_uid);
+  auto ps_iter = m_ps_cache.shader_map.find(ps_uid);
   if (ps_iter != m_ps_cache.shader_map.end() && !ps_iter->second.pending)
     ps = ps_iter->second.shader.get();
   else
-    ps = InsertPixelShader(config.ps_uid, CompilePixelShader(config.ps_uid));
+    ps = InsertPixelShader(ps_uid, CompilePixelShader(ps_uid));
 
   if (!vs || !ps)
     return {};
@@ -492,12 +495,15 @@ ShaderCache::GetGXUberPipelineConfig(const GXUberPipelineUid& config)
   else
     vs = InsertVertexUberShader(config.vs_uid, CompileVertexUberShader(config.vs_uid));
 
+  UberShader::PixelShaderUid ps_uid = config.ps_uid;
+  UberShader::ClearUnusedPixelShaderUidBits(m_api_type, m_host_config, &ps_uid);
+
   const AbstractShader* ps;
-  auto ps_iter = m_uber_ps_cache.shader_map.find(config.ps_uid);
+  auto ps_iter = m_uber_ps_cache.shader_map.find(ps_uid);
   if (ps_iter != m_uber_ps_cache.shader_map.end() && !ps_iter->second.pending)
     ps = ps_iter->second.shader.get();
   else
-    ps = InsertPixelUberShader(config.ps_uid, CompilePixelUberShader(config.ps_uid));
+    ps = InsertPixelUberShader(ps_uid, CompilePixelUberShader(ps_uid));
 
   if (!vs || !ps)
     return {};
@@ -802,10 +808,13 @@ void ShaderCache::QueuePipelineCompile(const GXPipelineUid& uid, u32 priority)
       if (vs_it == shader_cache->m_vs_cache.shader_map.end())
         shader_cache->QueueVertexShaderCompile(uid.vs_uid, priority);
 
-      auto ps_it = shader_cache->m_ps_cache.shader_map.find(uid.ps_uid);
+      PixelShaderUid ps_uid = uid.ps_uid;
+      ClearUnusedPixelShaderUidBits(shader_cache->m_api_type, shader_cache->m_host_config, &ps_uid);
+
+      auto ps_it = shader_cache->m_ps_cache.shader_map.find(ps_uid);
       stages_ready &= ps_it != shader_cache->m_ps_cache.shader_map.end() && !ps_it->second.pending;
       if (ps_it == shader_cache->m_ps_cache.shader_map.end())
-        shader_cache->QueuePixelShaderCompile(uid.ps_uid, priority);
+        shader_cache->QueuePixelShaderCompile(ps_uid, priority);
 
       return stages_ready;
     }
@@ -870,11 +879,15 @@ void ShaderCache::QueueUberPipelineCompile(const GXUberPipelineUid& uid, u32 pri
       if (vs_it == shader_cache->m_uber_vs_cache.shader_map.end())
         shader_cache->QueueVertexUberShaderCompile(uid.vs_uid, priority);
 
-      auto ps_it = shader_cache->m_uber_ps_cache.shader_map.find(uid.ps_uid);
+      UberShader::PixelShaderUid ps_uid = uid.ps_uid;
+      UberShader::ClearUnusedPixelShaderUidBits(shader_cache->m_api_type,
+                                                shader_cache->m_host_config, &ps_uid);
+
+      auto ps_it = shader_cache->m_uber_ps_cache.shader_map.find(ps_uid);
       stages_ready &=
           ps_it != shader_cache->m_uber_ps_cache.shader_map.end() && !ps_it->second.pending;
       if (ps_it == shader_cache->m_uber_ps_cache.shader_map.end())
-        shader_cache->QueuePixelUberShaderCompile(uid.ps_uid, priority);
+        shader_cache->QueuePixelUberShaderCompile(ps_uid, priority);
 
       return stages_ready;
     }
diff --git a/Source/Core/VideoCommon/UberShaderPixel.cpp b/Source/Core/VideoCommon/UberShaderPixel.cpp
index 4b680fee2e..8eff68f14b 100644
--- a/Source/Core/VideoCommon/UberShaderPixel.cpp
+++ b/Source/Core/VideoCommon/UberShaderPixel.cpp
@@ -29,7 +29,8 @@ PixelShaderUid GetPixelShaderUid()
   return out;
 }
 
-void ClearUnusedPixelShaderUidBits(APIType ApiType, PixelShaderUid* uid)
+void ClearUnusedPixelShaderUidBits(APIType ApiType, const ShaderHostConfig& host_config,
+                                   PixelShaderUid* uid)
 {
   pixel_ubershader_uid_data* uid_data = uid->GetUidData<pixel_ubershader_uid_data>();
 
diff --git a/Source/Core/VideoCommon/UberShaderPixel.h b/Source/Core/VideoCommon/UberShaderPixel.h
index 5bacf68a43..344cc4e032 100644
--- a/Source/Core/VideoCommon/UberShaderPixel.h
+++ b/Source/Core/VideoCommon/UberShaderPixel.h
@@ -29,5 +29,6 @@ ShaderCode GenPixelShader(APIType ApiType, const ShaderHostConfig& host_config,
                           const pixel_ubershader_uid_data* uid_data);
 
 void EnumeratePixelShaderUids(const std::function<void(const PixelShaderUid&)>& callback);
-void ClearUnusedPixelShaderUidBits(APIType ApiType, PixelShaderUid* uid);
+void ClearUnusedPixelShaderUidBits(APIType ApiType, const ShaderHostConfig& host_config,
+                                   PixelShaderUid* uid);
 }