diff --git a/onnxruntime/core/providers/qnn/builder/qnn_backend_manager.cc b/onnxruntime/core/providers/qnn/builder/qnn_backend_manager.cc
index eba0a8c2615aa..3f2ceb0f3d417 100644
--- a/onnxruntime/core/providers/qnn/builder/qnn_backend_manager.cc
+++ b/onnxruntime/core/providers/qnn/builder/qnn_backend_manager.cc
@@ -1367,7 +1367,8 @@ Status QnnBackendManager::LoadCachedQnnContextFromBuffer(char* buffer, uint64_t
 
   void* bin_buffer = nullptr;
 #ifdef QNN_FILE_MAPPED_WEIGHTS_AVAILABLE
-  if (file_mapped_weights_enabled_) {
+  // A nonzero buffer length implies an embedded context
+  if (file_mapped_weights_enabled_ && buffer_length == 0) {
     ORT_RETURN_IF(!file_mapper_, "Attemping to use File Mapping feature but file_mapper_ is uninitialized");
 
     ORT_RETURN_IF_ERROR(GetFileSizeIfValid(context_bin_filepath, buffer_length));
diff --git a/onnxruntime/core/providers/qnn/qnn_execution_provider.cc b/onnxruntime/core/providers/qnn/qnn_execution_provider.cc
index 7d9de02654230..6be50ac4da5c3 100644
--- a/onnxruntime/core/providers/qnn/qnn_execution_provider.cc
+++ b/onnxruntime/core/providers/qnn/qnn_execution_provider.cc
@@ -488,6 +488,11 @@ QNNExecutionProvider::QNNExecutionProvider(const ProviderOptions& provider_optio
   enable_file_mapped_weights_ = false;
   LOGS_DEFAULT(WARNING) << "File mapped weights feature is only available on Windows arm64 devices for QNN API versions >= 2.32. "
                         << "Feature will be disabled by default";
+#else
+  if (qnn_context_embed_mode_ && enable_file_mapped_weights_) {
+    enable_file_mapped_weights_ = false;
+    LOGS_DEFAULT(WARNING) << "File mapped weights feature is incompatible with embedded EP contexts. Feature will be disabled by default.";
+  }
 #endif
 
   static const std::string QNN_DEVICE_ID = "device_id";