diff --git a/src/xenia/gpu/d3d12/d3d12_command_processor.cc b/src/xenia/gpu/d3d12/d3d12_command_processor.cc
index 9e549d19b..8f7f6d7b2 100644
--- a/src/xenia/gpu/d3d12/d3d12_command_processor.cc
+++ b/src/xenia/gpu/d3d12/d3d12_command_processor.cc
@@ -3045,8 +3045,6 @@ bool D3D12CommandProcessor::EndSubmission(bool is_swap) {
 
       texture_cache_->ClearCache();
 
-      pipeline_cache_->ClearCache();
-
       for (auto it : root_signatures_bindful_) {
         it.second->Release();
       }
diff --git a/src/xenia/gpu/d3d12/pipeline_cache.cc b/src/xenia/gpu/d3d12/pipeline_cache.cc
index bd089c30b..9b6cd845b 100644
--- a/src/xenia/gpu/d3d12/pipeline_cache.cc
+++ b/src/xenia/gpu/d3d12/pipeline_cache.cc
@@ -175,9 +175,8 @@ bool PipelineCache::Initialize() {
 }
 
 void PipelineCache::Shutdown() {
-  ClearCache(true);
-
-  // Shut down all threads.
+  // Shut down all threads, before destroying the pipelines since they may be
+  // creating them.
   if (!creation_threads_.empty()) {
     {
       std::lock_guard<std::mutex> lock(creation_request_lock_);
@@ -191,44 +190,11 @@ void PipelineCache::Shutdown() {
   }
   creation_completion_event_.reset();
 
-  ui::d3d12::util::ReleaseAndNull(dxc_compiler_);
-  ui::d3d12::util::ReleaseAndNull(dxc_utils_);
-  ui::d3d12::util::ReleaseAndNull(dxbc_converter_);
-}
-
-void PipelineCache::ClearCache(bool shutting_down) {
-  bool reinitialize_shader_storage =
-      !shutting_down && storage_write_thread_ != nullptr;
-  std::filesystem::path shader_storage_cache_root;
-  uint32_t shader_storage_title_id = shader_storage_title_id_;
-  if (reinitialize_shader_storage) {
-    shader_storage_cache_root = shader_storage_cache_root_;
-  }
+  // Shut down the persistent shader / pipeline storage.
   ShutdownShaderStorage();
 
-  // Remove references to the current pipeline.
-  current_pipeline_ = nullptr;
-
-  if (!creation_threads_.empty()) {
-    // Empty the pipeline creation queue and make sure there are no threads
-    // currently creating pipelines because pipelines are going to be deleted.
-    bool await_creation_completion_event = false;
-    {
-      std::lock_guard<std::mutex> lock(creation_request_lock_);
-      creation_queue_.clear();
-      await_creation_completion_event = creation_threads_busy_ != 0;
-      if (await_creation_completion_event) {
-        creation_completion_event_->Reset();
-        creation_completion_set_event_ = true;
-      }
-    }
-    if (await_creation_completion_event) {
-      creation_request_cond_.notify_one();
-      xe::threading::Wait(creation_completion_event_.get(), false);
-    }
-  }
-
   // Destroy all pipelines.
+  current_pipeline_ = nullptr;
   for (auto it : pipelines_) {
     it.second->state->Release();
     delete it.second;
@@ -250,10 +216,10 @@ void PipelineCache::ClearCache(bool shutting_down) {
   shaders_.clear();
   shader_storage_index_ = 0;
 
-  if (reinitialize_shader_storage) {
-    InitializeShaderStorage(shader_storage_cache_root, shader_storage_title_id,
-                            false);
-  }
+  // Shut down shader translation.
+  ui::d3d12::util::ReleaseAndNull(dxc_compiler_);
+  ui::d3d12::util::ReleaseAndNull(dxc_utils_);
+  ui::d3d12::util::ReleaseAndNull(dxbc_converter_);
 }
 
 void PipelineCache::InitializeShaderStorage(
diff --git a/src/xenia/gpu/d3d12/pipeline_cache.h b/src/xenia/gpu/d3d12/pipeline_cache.h
index f60dff1f6..8f19858d7 100644
--- a/src/xenia/gpu/d3d12/pipeline_cache.h
+++ b/src/xenia/gpu/d3d12/pipeline_cache.h
@@ -55,7 +55,10 @@ class PipelineCache {
 
   bool Initialize();
   void Shutdown();
-  void ClearCache(bool shutting_down = false);
+  // No ClearCache because it's undesirable with the persistent shader storage
+  // (if the storage is reloaded, effectively nothing is cleared, while the call
+  // takes a long time, and if it's not, there will be heavy stuttering for the
+  // rest of the execution of the guest).
 
   void InitializeShaderStorage(const std::filesystem::path& cache_root,
                                uint32_t title_id, bool blocking);