diff --git a/tools/ci_build/build.py b/tools/ci_build/build.py
index 55afbd6aa0..a7aad69be5 100644
--- a/tools/ci_build/build.py
+++ b/tools/ci_build/build.py
@@ -2773,7 +2773,17 @@ def main():
     args = parse_arguments()
 
     print(args)
-
+    if args.build_wasm:
+        # No custom triplet for the wasm builds yet
+        args.use_vcpkg = False
+    elif args.minimal_build is not None:
+        # Minimal build uses a custom ONNX cmake file. Don't know how to deal with it yet
+        args.use_vcpkg = False
+    elif args.ios or args.macos == "Catalyst":
+        args.use_vcpkg = False
+    elif not args.use_vcpkg:
+        sys.exit(1)
+        
     if os.getenv("ORT_BUILD_WITH_CACHE") == "1":
         args.use_cache = True
 
diff --git a/tools/ci_build/github/azure-pipelines/win-gpu-webgpu-ci-pipeline.yml b/tools/ci_build/github/azure-pipelines/win-gpu-webgpu-ci-pipeline.yml
index bb6c210161..c339504cb2 100644
--- a/tools/ci_build/github/azure-pipelines/win-gpu-webgpu-ci-pipeline.yml
+++ b/tools/ci_build/github/azure-pipelines/win-gpu-webgpu-ci-pipeline.yml
@@ -47,6 +47,7 @@ stages:
         additionalBuildFlags: >-
           --build_nodejs
           --use_webgpu
+          --use_vcpkg
           --cmake_extra_defines onnxruntime_BUILD_UNIT_TESTS=ON onnxruntime_BUILD_DAWN_MONOLITHIC_LIBRARY=ON
         msbuildPlatform: x64
         isX86: false
@@ -91,7 +92,7 @@ stages:
             Today: $(TODAY)
             CacheDir: $(ORT_CACHE_DIR)
             AdditionalKey: " $(System.StageName) | RelWithDebInfo "
-            BuildPyArguments: '--config RelWithDebInfo --build_dir $(Build.BinariesDirectory) --skip_submodule_sync --update --parallel --cmake_generator "Visual Studio 17 2022" --use_webgpu --use_external_dawn --skip_tests --target onnxruntime_webgpu_external_dawn_test'
+            BuildPyArguments: '--use_vcpkg --config RelWithDebInfo --build_dir $(Build.BinariesDirectory) --skip_submodule_sync --update --parallel --cmake_generator "Visual Studio 17 2022" --use_webgpu --use_external_dawn --skip_tests --target onnxruntime_webgpu_external_dawn_test'
             MsbuildArguments: '-maxcpucount'
             BuildArch: x64
             Platform: x64