diff --git a/src/coreclr/nativeaot/BuildIntegration/Microsoft.NETCore.Native.Publish.targets b/src/coreclr/nativeaot/BuildIntegration/Microsoft.NETCore.Native.Publish.targets
index c1ca1fae10f4c3..2886dea53281b1 100644
--- a/src/coreclr/nativeaot/BuildIntegration/Microsoft.NETCore.Native.Publish.targets
+++ b/src/coreclr/nativeaot/BuildIntegration/Microsoft.NETCore.Native.Publish.targets
@@ -40,6 +40,8 @@
   <UsingTask TaskName="ComputeManagedAssembliesToCompileToNative" AssemblyFile="$(IlcBuildTasksPath)" />
   <Target Name="_ComputeAssembliesToCompileToNative" DependsOnTargets="$(IlcDynamicBuildPropertyDependencies)">
 
+    <Warning Condition="Exists($(UserRuntimeConfig))" Text="The published project has a runtimeconfig.template.json that is not supported by PublishAot. Move the configuration to the project file using RuntimeHostConfigurationOption." />
+    
     <!-- Fail with descriptive error message for common mistake. -->
     <Error Condition="$([MSBuild]::VersionLessThan('$(NETCoreSdkVersion)', '6.0.0'))" Text=".NET SDK 6+ is required for native compilation." />
     <Error Condition="$([MSBuild]::VersionLessThan('$(TargetFrameworkVersion)', '6.0'))" Text="For native compilation, the project needs to target .NET 6 or higher." />