diff --git a/csharp/src/Microsoft.AI.MachineLearning.Interop/Microsoft.AI.MachineLearning.targets b/csharp/src/Microsoft.AI.MachineLearning.Interop/Microsoft.AI.MachineLearning.targets
index 68a53643b5..9477e7ef89 100644
--- a/csharp/src/Microsoft.AI.MachineLearning.Interop/Microsoft.AI.MachineLearning.targets
+++ b/csharp/src/Microsoft.AI.MachineLearning.Interop/Microsoft.AI.MachineLearning.targets
@@ -9,10 +9,11 @@
   </PropertyGroup>
 
   <PropertyGroup>
-    <RuntimesDirectory Condition="'$(OutputType)' == 'AppContainerExe'">$(MSBuildThisFileDirectory)..\..\runtimes\win-$(WindowsAI-Platform)\uap</RuntimesDirectory>
-    <RuntimesDirectory Condition="'$(RuntimesDirectory)' == ''">$(MSBuildThisFileDirectory)..\..\runtimes\win-$(WindowsAI-Platform)\native</RuntimesDirectory>
-    <WindowsAIBinary>$(RuntimesDirectory)\Microsoft.AI.MachineLearning.dll</WindowsAIBinary>
-    <OnnxRuntimeBinary>$(RuntimesDirectory)\onnxruntime.dll</OnnxRuntimeBinary>
+    <RuntimesDirectory Condition="'$(TargetPlatformIdentifier)' == 'UAP'">$(MSBuildThisFileDirectory)..\..\runtimes\win-$(WindowsAI-Platform)\lib\uap10.0</RuntimesDirectory>
+    <RuntimesDirectory Condition="'$(TargetPlatformIdentifier)' != 'UAP'">$(MSBuildThisFileDirectory)..\..\runtimes\win-$(WindowsAI-Platform)\_native</RuntimesDirectory>
+    <WindowsAIBinarySubfolder Condition="'$(UseWindowsMLStaticRuntime)' == 'true'">static\</WindowsAIBinarySubfolder>
+    <WindowsAIBinary>$(RuntimesDirectory)\$(WindowsAIBinarySubfolder)Microsoft.AI.MachineLearning.dll</WindowsAIBinary>
+    <OnnxRuntimeBinary>$(RuntimesDirectory)\$(WindowsAIBinarySubfolder)onnxruntime.dll</OnnxRuntimeBinary>
   </PropertyGroup>
 
   <Target Name="CopyMLBinaries" BeforeTargets="CoreBuild">
diff --git a/csharp/src/Microsoft.AI.MachineLearning/Microsoft.AI.MachineLearning.targets b/csharp/src/Microsoft.AI.MachineLearning/Microsoft.AI.MachineLearning.targets
index 807cf89e30..9730fa9610 100644
--- a/csharp/src/Microsoft.AI.MachineLearning/Microsoft.AI.MachineLearning.targets
+++ b/csharp/src/Microsoft.AI.MachineLearning/Microsoft.AI.MachineLearning.targets
@@ -6,10 +6,16 @@
   </PropertyGroup>
 
   <PropertyGroup>
-    <RuntimesDirectory Condition="'$(OutputType)' == 'AppContainerExe'">$(MSBuildThisFileDirectory)..\..\runtimes\win-$(WindowsAI-Platform)\uap</RuntimesDirectory>
-    <RuntimesDirectory Condition="'$(RuntimesDirectory)' == ''">$(MSBuildThisFileDirectory)..\..\runtimes\win-$(WindowsAI-Platform)\native</RuntimesDirectory>
+    <RuntimesDirectory Condition="'$(TargetPlatformIdentifier)' == 'UAP'">$(MSBuildThisFileDirectory)..\..\runtimes\win-$(WindowsAI-Platform)\lib\uap10.0</RuntimesDirectory>
+    <RuntimesDirectory Condition="'$(TargetPlatformIdentifier)' != 'UAP'">$(MSBuildThisFileDirectory)..\..\runtimes\win-$(WindowsAI-Platform)\_native</RuntimesDirectory>
     <WindowsAIBinarySubfolder Condition="'$(UseWindowsMLStaticRuntime)' == 'true'">static\</WindowsAIBinarySubfolder>
-    <WindowsAIBinary>$(RuntimesDirectory)\$(WindowsAIBinarySubfolder)Microsoft.AI.MachineLearning.dll</WindowsAIBinary>
+    <WindowsAIBinary>$(RuntimesDirectory)\$(WindowsAIBinarySubfolder)microsoft.ai.machinelearning.dll</WindowsAIBinary>
+    <WindowsAIWinMD>$(MSBuildThisFileDirectory)..\..\winmds\Microsoft.AI.MachineLearning.winmd</WindowsAIWinMD>
+    <WindowsAIExperimentalWinMD>$(MSBuildThisFileDirectory)..\..\winmds\Microsoft.AI.MachineLearning.Experimental.winmd</WindowsAIExperimentalWinMD>
+
+    <WindowsAIBinary>$([System.IO.Path]::GetFullPath($(WindowsAIBinary)))</WindowsAIBinary>
+    <WindowsAIWinMD>$([System.IO.Path]::GetFullPath($(WindowsAIWinMD)))</WindowsAIWinMD>
+    <WindowsAIExperimentalWinMD>$([System.IO.Path]::GetFullPath($(WindowsAIExperimentalWinMD)))</WindowsAIExperimentalWinMD>
   </PropertyGroup>
 
   <PropertyGroup Condition="'$(DisableOnnxRuntimeDllCopy)' != 'true'">
@@ -17,15 +23,15 @@
   </PropertyGroup>
   
   <ItemGroup>
-    <Reference Include="$(MSBuildThisFileDirectory)\..\..\lib\uap\Microsoft.AI.MachineLearning.winmd">
+    <Reference Include="$(WindowsAIWinMD)">
       <Implementation>$(WindowsAIBinary)</Implementation>
     </Reference>
-    <Reference Include="$(MSBuildThisFileDirectory)\..\..\lib\uap\Microsoft.AI.MachineLearning.Experimental.winmd">
+    <Reference Include="$(WindowsAIExperimentalWinMD)">
       <Implementation>$(WindowsAIBinary)</Implementation>
     </Reference>
   </ItemGroup>
 
-  <ItemGroup>
+  <ItemGroup Condition="'$(NuGetProjectStyle)' != 'PackageReference'">
     <ReferenceCopyLocalPaths Include="$(WindowsAIBinary);$(OnnxRuntimeBinary)" />
   </ItemGroup>
 </Project>
diff --git a/tools/ci_build/github/azure-pipelines/nuget/templates/windowsai.yml b/tools/ci_build/github/azure-pipelines/nuget/templates/windowsai.yml
index a90e58db88..c04f97358c 100644
--- a/tools/ci_build/github/azure-pipelines/nuget/templates/windowsai.yml
+++ b/tools/ci_build/github/azure-pipelines/nuget/templates/windowsai.yml
@@ -322,30 +322,30 @@ jobs:
         $arm_static_runtime_nupkg_unzipped_directory = [System.IO.Path]::Combine($arm_static_runtime_nupkg_unzipped_directory_root, 'binaries', [System.IO.Path]::GetFileNameWithoutExtension($arm_static_runtime_nuget_package))
         [System.IO.Compression.ZipFile]::ExtractToDirectory($arm_static_runtime_nuget_package, $arm_static_runtime_nupkg_unzipped_directory)
 
-        $x64_store_runtime_path_old = [System.IO.Path]::Combine($x64_store_nupkg_unzipped_directory, 'runtimes', 'win-x64', 'uap')
-        $x64_store_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-x64', 'uap')
-        $x64_static_runtime_path_old = [System.IO.Path]::Combine($x64_static_runtime_nupkg_unzipped_directory, 'runtimes', 'win-x64', 'native')
-        $x64_static_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-x64', 'native', 'static')
-        $x86_runtime_path_old = [System.IO.Path]::Combine($x86_nupkg_unzipped_directory, 'runtimes', 'win-x86', 'native')
-        $x86_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-x86', 'native')
-        $x86_store_runtime_path_old = [System.IO.Path]::Combine($x86_store_nupkg_unzipped_directory, 'runtimes', 'win-x86', 'uap')
-        $x86_store_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-x86', 'uap')
-        $x86_static_runtime_path_old = [System.IO.Path]::Combine($x86_static_runtime_nupkg_unzipped_directory, 'runtimes', 'win-x86', 'native')
-        $x86_static_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-x86', 'native', 'static')
-        $arm64_runtime_path_old = [System.IO.Path]::Combine($arm64_nupkg_unzipped_directory, 'runtimes', 'win-arm64', 'native')
-        $arm64_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-arm64', 'native')
-        $arm64_store_runtime_path_old = [System.IO.Path]::Combine($arm64_store_nupkg_unzipped_directory, 'runtimes', 'win-arm64', 'uap')
-        $arm64_store_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-arm64', 'uap')
-        $arm64_static_runtime_path_old = [System.IO.Path]::Combine($arm64_static_runtime_nupkg_unzipped_directory, 'runtimes', 'win-arm64', 'native')
-        $arm64_static_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-arm64', 'native', 'static')
-        $arm_runtime_path_old = [System.IO.Path]::Combine($arm_nupkg_unzipped_directory, 'runtimes', 'win-arm', 'native')
-        $arm_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-arm', 'native')
-        $arm_store_runtime_path_old = [System.IO.Path]::Combine($arm_store_nupkg_unzipped_directory, 'runtimes', 'win-arm', 'uap')
-        $arm_store_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-arm', 'uap')
-        $arm_static_runtime_path_old = [System.IO.Path]::Combine($arm_static_runtime_nupkg_unzipped_directory, 'runtimes', 'win-arm', 'native')
-        $arm_static_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-arm', 'native', 'static')
-        $uap_build_path_old = [System.IO.Path]::Combine($x64_store_nupkg_unzipped_directory, 'build', 'uap')
-        $uap_build_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'build', 'uap')
+        $x64_store_runtime_path_old = [System.IO.Path]::Combine($x64_store_nupkg_unzipped_directory, 'runtimes', 'win-x64', 'lib\\uap10.0')
+        $x64_store_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-x64', 'lib\\uap10.0')
+        $x64_static_runtime_path_old = [System.IO.Path]::Combine($x64_static_runtime_nupkg_unzipped_directory, 'runtimes', 'win-x64', '_native')
+        $x64_static_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-x64', '_native', 'static')
+        $x86_runtime_path_old = [System.IO.Path]::Combine($x86_nupkg_unzipped_directory, 'runtimes', 'win-x86', '_native')
+        $x86_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-x86', '_native')
+        $x86_store_runtime_path_old = [System.IO.Path]::Combine($x86_store_nupkg_unzipped_directory, 'runtimes', 'win-x86', 'lib\\uap10.0')
+        $x86_store_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-x86', 'lib\\uap10.0')
+        $x86_static_runtime_path_old = [System.IO.Path]::Combine($x86_static_runtime_nupkg_unzipped_directory, 'runtimes', 'win-x86', '_native')
+        $x86_static_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-x86', '_native', 'static')
+        $arm64_runtime_path_old = [System.IO.Path]::Combine($arm64_nupkg_unzipped_directory, 'runtimes', 'win-arm64', '_native')
+        $arm64_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-arm64', '_native')
+        $arm64_store_runtime_path_old = [System.IO.Path]::Combine($arm64_store_nupkg_unzipped_directory, 'runtimes', 'win-arm64', 'lib\\uap10.0')
+        $arm64_store_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-arm64', 'lib\\uap10.0')
+        $arm64_static_runtime_path_old = [System.IO.Path]::Combine($arm64_static_runtime_nupkg_unzipped_directory, 'runtimes', 'win-arm64', '_native')
+        $arm64_static_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-arm64', '_native', 'static')
+        $arm_runtime_path_old = [System.IO.Path]::Combine($arm_nupkg_unzipped_directory, 'runtimes', 'win-arm', '_native')
+        $arm_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-arm', '_native')
+        $arm_store_runtime_path_old = [System.IO.Path]::Combine($arm_store_nupkg_unzipped_directory, 'runtimes', 'win-arm', 'lib\\uap10.0')
+        $arm_store_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-arm', 'lib\\uap10.0')
+        $arm_static_runtime_path_old = [System.IO.Path]::Combine($arm_static_runtime_nupkg_unzipped_directory, 'runtimes', 'win-arm', '_native')
+        $arm_static_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-arm', '_native', 'static')
+        $uap_build_path_old = [System.IO.Path]::Combine($x64_store_nupkg_unzipped_directory, 'build', 'uap10.0')
+        $uap_build_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'build', 'uap10.0')
 
         New-Item -Path $x64_store_runtime_path_new -ItemType Directory
         New-Item -Path $x64_static_runtime_path_new -ItemType Directory
@@ -469,12 +469,12 @@ jobs:
         $arm_nupkg_unzipped_directory = [System.IO.Path]::Combine($arm_nupkg_unzipped_directory_root, 'symbols', [System.IO.Path]::GetFileNameWithoutExtension($arm_nuget_package))
         [System.IO.Compression.ZipFile]::ExtractToDirectory($arm_nuget_package, $arm_nupkg_unzipped_directory)
 
-        $x86_runtime_path_old = [System.IO.Path]::Combine($x86_nupkg_unzipped_directory, 'runtimes', 'win-x86', 'native')
-        $x86_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-x86', 'native')
-        $arm64_runtime_path_old = [System.IO.Path]::Combine($arm64_nupkg_unzipped_directory, 'runtimes', 'win-arm64', 'native')
-        $arm64_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-arm64', 'native')
-        $arm_runtime_path_old = [System.IO.Path]::Combine($arm_nupkg_unzipped_directory, 'runtimes', 'win-arm', 'native')
-        $arm_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-arm', 'native')
+        $x86_runtime_path_old = [System.IO.Path]::Combine($x86_nupkg_unzipped_directory, 'runtimes', 'win-x86', '_native')
+        $x86_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-x86', '_native')
+        $arm64_runtime_path_old = [System.IO.Path]::Combine($arm64_nupkg_unzipped_directory, 'runtimes', 'win-arm64', '_native')
+        $arm64_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-arm64', '_native')
+        $arm_runtime_path_old = [System.IO.Path]::Combine($arm_nupkg_unzipped_directory, 'runtimes', 'win-arm', '_native')
+        $arm_runtime_path_new = [System.IO.Path]::Combine($x64_nupkg_unzipped_directory, 'runtimes', 'win-arm', '_native')
 
         New-Item -Path $x86_runtime_path_new -ItemType Directory
         New-Item -Path $arm64_runtime_path_new -ItemType Directory
diff --git a/tools/nuget/generate_nuspec_for_native_nuget.py b/tools/nuget/generate_nuspec_for_native_nuget.py
index 846c69ece1..256c7a7d0e 100644
--- a/tools/nuget/generate_nuspec_for_native_nuget.py
+++ b/tools/nuget/generate_nuspec_for_native_nuget.py
@@ -216,9 +216,14 @@ def generate_files(list, args):
         copy_command = "cp"
         runtimes_target = '" target="runtimes\\linux-'
 
+    if is_windowsai_package:
+        runtimes_native_folder = '_native'
+    else:
+        runtimes_native_folder = 'native'
+
     runtimes = '{}{}\\{}"'.format(runtimes_target,
                                   args.target_architecture,
-                                  'uap' if args.is_store_build else 'native')
+                                  'lib\\uap10.0' if args.is_store_build else runtimes_native_folder)
 
     # Process headers
     files_list.append('<file src=' + '"' + os.path.join(args.sources_path,
@@ -277,11 +282,11 @@ def generate_files(list, args):
         # Process microsoft.ai.machinelearning.winmd
         files_list.append('<file src=' + '"' + os.path.join(args.ort_build_path, args.build_config,
                                                             'microsoft.ai.machinelearning.winmd') +
-                          '" target="lib\\uap\\Microsoft.AI.MachineLearning.winmd" />')
+                          '" target="winmds\\Microsoft.AI.MachineLearning.winmd" />')
         # Process microsoft.ai.machinelearning.experimental.winmd
         files_list.append('<file src=' + '"' + os.path.join(args.ort_build_path, args.build_config,
                                                             'microsoft.ai.machinelearning.experimental.winmd') +
-                          '" target="lib\\uap\\Microsoft.AI.MachineLearning.Experimental.winmd" />')
+                          '" target="winmds\\Microsoft.AI.MachineLearning.Experimental.winmd" />')
         if args.target_architecture == 'x64' and not args.is_store_build:
             interop_dll_path = 'Microsoft.AI.MachineLearning.Interop\\net5.0-windows10.0.19041.0'
             interop_dll = interop_dll_path + '\\Microsoft.AI.MachineLearning.Interop.dll'
@@ -312,17 +317,17 @@ def generate_files(list, args):
         files_list.append('<file src=' + '"' +
                           os.path.join(args.native_build_path, 'microsoft.ai.machinelearning.lib') +
                           runtimes_target + args.target_architecture + '\\' +
-                          ('uap' if args.is_store_build else 'native') +
+                          ('lib\\uap10.0' if args.is_store_build else '_native') +
                           '\\Microsoft.AI.MachineLearning.lib" />')
         files_list.append('<file src=' + '"' + os.path.join(args.native_build_path,
                                                             'microsoft.ai.machinelearning.dll') +
                           runtimes_target + args.target_architecture + '\\' +
-                          ('uap' if args.is_store_build else 'native') +
+                          ('lib\\uap10.0' if args.is_store_build else '_native') +
                           '\\Microsoft.AI.MachineLearning.dll" />')
         files_list.append('<file src=' + '"' + os.path.join(args.native_build_path,
                                                             'microsoft.ai.machinelearning.pdb') +
                           runtimes_target + args.target_architecture + '\\' +
-                          ('uap' if args.is_store_build else 'native') +
+                          ('lib\\uap10.0' if args.is_store_build else '_native') +
                           '\\Microsoft.AI.MachineLearning.pdb" />')
     # Process execution providers which are built as shared libs
     if args.execution_provider == "tensorrt":
@@ -398,7 +403,7 @@ def generate_files(list, args):
         windowsai_rules = 'Microsoft.AI.MachineLearning.Rules.Project.xml'
         windowsai_native_rules = os.path.join(args.sources_path, 'csharp', 'src', windowsai_src, windowsai_rules)
         windowsai_native_targets = os.path.join(args.sources_path, 'csharp', 'src', windowsai_src, windowsai_targets)
-        build = 'build\\{}'.format('uap' if args.is_store_build else 'native')
+        build = 'build\\{}'.format('uap10.0' if args.is_store_build else 'native')
         files_list.append('<file src=' + '"' + windowsai_native_props + '" target="' + build + '" />')
         # Process native targets
         files_list.append('<file src=' + '"' + windowsai_native_targets + '" target="' + build + '" />')
diff --git a/tools/nuget/validate_nuget.py b/tools/nuget/validate_nuget.py
index 9eeb178718..77b916d79f 100644
--- a/tools/nuget/validate_nuget.py
+++ b/tools/nuget/validate_nuget.py
@@ -33,11 +33,12 @@ def is_windows():
     return sys.platform.startswith("win")
 
 
-def check_if_dlls_are_present(platforms_supported, zip_file):
+def check_if_dlls_are_present(is_windows_ai_package, platforms_supported, zip_file):
     platforms = platforms_supported.strip().split(",")
     for platform in platforms:
         if platform.startswith("win"):
-            path = "runtimes/" + platform + "/native/onnxruntime.dll"
+            native_folder = '_native' if is_windows_ai_package else 'native'
+            path = "runtimes/" + platform + "/" + native_folder + "/onnxruntime.dll"
             print('Checking path: ' + path)
             if (path not in zip_file.namelist()):
                 print("onnxruntime.dll not found for " + platform)
@@ -109,7 +110,7 @@ def main():
             raise Exception('Nuget validation is currently supported only on Windows')
 
         # Make a copy of the Nuget package
-        print('Making a copy of the Nuget and extracting its contents')
+        print('Copying [' + full_nuget_path + '] -> [' + nupkg_copy_name + '], and extracting its contents')
         os.system("copy " + full_nuget_path + " " + nupkg_copy_name)
 
         # Convert nupkg to zip
@@ -118,7 +119,8 @@ def main():
 
         # Check if the relevant dlls are present in the Nuget/Zip
         print('Checking if the Nuget contains relevant dlls')
-        check_if_dlls_are_present(args.platforms_supported, zip_file)
+        is_windows_ai_package = os.path.basename(full_nuget_path).startswith('Microsoft.AI.MachineLearning')
+        check_if_dlls_are_present(is_windows_ai_package, args.platforms_supported, zip_file)
 
         # Check if the Nuget has been signed
         if (args.verify_nuget_signing != 'true' and args.verify_nuget_signing != 'false'):