diff --git a/js/web/lib/wasm/jsep/backend-webnn.ts b/js/web/lib/wasm/jsep/backend-webnn.ts
index d510972c236f0..6cad192479625 100644
--- a/js/web/lib/wasm/jsep/backend-webnn.ts
+++ b/js/web/lib/wasm/jsep/backend-webnn.ts
@@ -8,37 +8,25 @@
 
 import {Tensor} from 'onnxruntime-common';
 
+import {DataType} from '../wasm-common';
+import {getInstance} from '../wasm-factory';
+
 import {createView} from './tensor-view';
 import {BufferId, BufferManager, createBufferManager} from './webnn/buffer-manager';
 
-/*
- * TensorProto::data_type from the ONNX specification.
- */
-enum TensorProtoDataType {
-  float = 1,
-  uint8 = 2,
-  int8 = 3,
-  int32 = 6,
-  int64 = 7,
-  bool = 9,
-  float16 = 10,
-  uint32 = 12,
-  uint64 = 13,
-}
-
 /*
  * TensorProto::data_type to WebNN OperandType mapping.
  */
-const onnxDataTypeToWebnnDataType = new Map<TensorProtoDataType, MLOperandDataType>([
-  [TensorProtoDataType.float, 'float32'],
-  [TensorProtoDataType.float16, 'float16'],
-  [TensorProtoDataType.int32, 'int32'],
-  [TensorProtoDataType.uint32, 'uint32'],
-  [TensorProtoDataType.int64, 'int64'],
-  [TensorProtoDataType.uint64, 'uint64'],
-  [TensorProtoDataType.int8, 'int8'],
-  [TensorProtoDataType.uint8, 'uint8'],
-  [TensorProtoDataType.bool, 'uint8'],
+const onnxDataTypeToWebnnDataType = new Map<DataType, MLOperandDataType>([
+  [DataType.float, 'float32'],
+  [DataType.float16, 'float16'],
+  [DataType.int32, 'int32'],
+  [DataType.uint32, 'uint32'],
+  [DataType.int64, 'int64'],
+  [DataType.uint64, 'uint64'],
+  [DataType.int8, 'int8'],
+  [DataType.uint8, 'uint8'],
+  [DataType.bool, 'uint8'],
 ]);
 
 /**
@@ -130,6 +118,10 @@ export class WebNNBackend {
   }
 
   public uploadBuffer(bufferId: BufferId, data: Uint8Array): void {
+    const wasm = getInstance();
+    if (!wasm.shouldTransferToMLBuffer) {
+      throw new Error('Trying to upload to a MLBuffer while shouldTransferToMLBuffer is false');
+    }
     this.bufferManager.upload(bufferId, data);
   }
 
diff --git a/js/web/lib/wasm/wasm-core-impl.ts b/js/web/lib/wasm/wasm-core-impl.ts
index b23518dd20e73..43d2980de1c9f 100644
--- a/js/web/lib/wasm/wasm-core-impl.ts
+++ b/js/web/lib/wasm/wasm-core-impl.ts
@@ -261,6 +261,7 @@ export const createSession = async(
     for (const provider of options?.executionProviders ?? []) {
       const providerName = typeof provider === 'string' ? provider : provider.name;
       if (providerName === 'webnn') {
+        wasm.shouldTransferToMLBuffer = false;
         if (wasm.currentContext) {
           throw new Error('WebNN execution provider is already set.');
         }
@@ -294,6 +295,7 @@ export const createSession = async(
     if (wasm.currentContext) {
       wasm.jsepRegisterMLContext!(sessionHandle, wasm.currentContext);
       wasm.currentContext = undefined;
+      wasm.shouldTransferToMLBuffer = true;
     }
 
     const [inputCount, outputCount] = getSessionInputOutputCount(sessionHandle);
@@ -691,16 +693,19 @@ export const run = async(
               'gpu-buffer'
             ]);
           } else if (preferredLocation === 'ml-buffer' && size > 0) {
-            const getMLBuffer = wasm.jsepGetMLBuffer;
-            if (!getMLBuffer) {
+            const ensureBuffer = wasm.jsepEnsureBuffer;
+            if (!ensureBuffer) {
               throw new Error('preferredLocation "ml-buffer" is not supported without using WebNN.');
             }
-            const mlBuffer = getMLBuffer(dataOffset);
             const elementSize = getTensorElementSize(dataType);
             if (elementSize === undefined || !isMLBufferSupportedType(type)) {
               throw new Error(`Unsupported data type: ${type}`);
             }
 
+            // If the graph has been partitioned, the output tensor may have not been created. For this reason, we use
+            // ensureBuffer to get/create the MLBuffer.
+            const mlBuffer = ensureBuffer(dataOffset, dataType, dims);
+
             // do not release the tensor right now. it will be released when user calls tensor.dispose().
             keepOutputTensor = true;
 
diff --git a/js/web/lib/wasm/wasm-types.ts b/js/web/lib/wasm/wasm-types.ts
index afca278422edd..783620b146364 100644
--- a/js/web/lib/wasm/wasm-types.ts
+++ b/js/web/lib/wasm/wasm-types.ts
@@ -126,6 +126,11 @@ export declare namespace JSEP {
      */
     currentContext: MLContext;
 
+    /**
+     * Disables creating MLBuffers. This is used to avoid creating MLBuffers for graph initializers.
+     */
+    shouldTransferToMLBuffer: boolean;
+
     /**
      * [exported from pre-jsep.js] Register MLContext for a session.
      * @param sessionId - specify the session ID.
diff --git a/onnxruntime/core/providers/webnn/allocator.cc b/onnxruntime/core/providers/webnn/allocator.cc
index 355ee7e48b9f4..4b8188a6f8344 100644
--- a/onnxruntime/core/providers/webnn/allocator.cc
+++ b/onnxruntime/core/providers/webnn/allocator.cc
@@ -12,6 +12,10 @@ void* WebNNBufferAllocator::Alloc(size_t size) {
   if (size == 0) {
     return nullptr;
   }
+  if (!emscripten::val::module_property("shouldTransferToMLBuffer").as<bool>()) {
+    // We don't need to transfer the buffer to an MLBuffer, so we don't need to allocate buffer id.
+    return nullptr;
+  }
   void* p = EM_ASM_PTR({ return Module.jsepReserveBufferId(); });
   allocations_[p] = size;
   stats_.num_allocs++;
diff --git a/onnxruntime/core/providers/webnn/data_transfer.cc b/onnxruntime/core/providers/webnn/data_transfer.cc
index 66096c74a7950..3ba9d1171191a 100644
--- a/onnxruntime/core/providers/webnn/data_transfer.cc
+++ b/onnxruntime/core/providers/webnn/data_transfer.cc
@@ -6,7 +6,6 @@
 #include <emscripten.h>
 #include "core/framework/tensor.h"
 
-
 namespace onnxruntime {
 namespace webnn {
 
@@ -24,6 +23,11 @@ common::Status DataTransfer::CopyTensor(const Tensor& src, Tensor& dst) const {
 
     const auto& dst_device = dst.Location().device;
 
+    if (!emscripten::val::module_property("shouldTransferToMLBuffer").as<bool>()) {
+      // We don't need to transfer the buffer to an MLBuffer, so we don't need to copy the buffer.
+      return Status::OK();
+    }
+
     if (dst_device.Type() == OrtDevice::GPU) {
       EM_ASM({
         Module.jsepUploadBuffer($0, HEAPU8.subarray($1, $1 + $2));