diff --git a/eng/testing/tests.singlefile.targets b/eng/testing/tests.singlefile.targets
index 6a50cbbfbf55a8..1a992b1b7e10d3 100644
--- a/eng/testing/tests.singlefile.targets
+++ b/eng/testing/tests.singlefile.targets
@@ -30,6 +30,12 @@
     <TrimmerSingleWarn>false</TrimmerSingleWarn>
     <StackTraceLineNumberSupport>true</StackTraceLineNumberSupport>
 
+    <!-- Use the SDK's ILCompilerTargetsPath hook to import ILC targets in the correct order
+         (before ILLink), matching how the shipping SDK imports them. -->
+    <PublishAot>true</PublishAot>
+    <_IlcReferencedAsPackage>false</_IlcReferencedAsPackage>
+    <ILCompilerTargetsPath>$(CoreCLRBuildIntegrationDir)Microsoft.DotNet.ILCompiler.SingleEntry.targets</ILCompilerTargetsPath>
+
     <!-- Forced by ILLink targets -->
     <SelfContained>true</SelfContained>
   </PropertyGroup>
@@ -42,8 +48,6 @@
     <DefineConstants>$(DefineConstants);TEST_READY_TO_RUN_COMPILED</DefineConstants>
   </PropertyGroup>
 
-  <Import Project="$(CoreCLRBuildIntegrationDir)Microsoft.DotNet.ILCompiler.SingleEntry.targets" Condition="'$(TestNativeAot)' == 'true'" />
-
   <ItemGroup Condition="'$(TestNativeAot)' == 'true'">
     <RdXmlFile Include="$(MSBuildThisFileDirectory)default.rd.xml" />
     <TrimmerRootAssembly Include="TestUtilities" Condition="'$(SkipTestUtilitiesReference)' != 'true'" />
diff --git a/src/coreclr/nativeaot/BuildIntegration/Microsoft.DotNet.ILCompiler.SingleEntry.targets b/src/coreclr/nativeaot/BuildIntegration/Microsoft.DotNet.ILCompiler.SingleEntry.targets
index cf313984696b5f..62cb2d8f7aadc4 100644
--- a/src/coreclr/nativeaot/BuildIntegration/Microsoft.DotNet.ILCompiler.SingleEntry.targets
+++ b/src/coreclr/nativeaot/BuildIntegration/Microsoft.DotNet.ILCompiler.SingleEntry.targets
@@ -42,7 +42,7 @@
   <PropertyGroup>
     <!-- If the NativeAOT toolchain is being consumed via package, runtime-specific properties must be set before compilation can proceed -->
     <ImportRuntimeIlcPackageTargetDependsOn>RunResolvePackageDependencies</ImportRuntimeIlcPackageTargetDependsOn>
-    <IlcSetupPropertiesDependsOn>ImportRuntimeIlcPackageTarget</IlcSetupPropertiesDependsOn>
+    <IlcSetupPropertiesDependsOn Condition="'$(_IlcReferencedAsPackage)' != 'false'">ImportRuntimeIlcPackageTarget</IlcSetupPropertiesDependsOn>
     <IlcDynamicBuildPropertyDependencies>SetupProperties</IlcDynamicBuildPropertyDependencies>
   </PropertyGroup>
 
@@ -62,7 +62,7 @@
   </Target>
 
   <!-- Locate the runtime package according to the current target runtime -->
-  <Target Name="ImportRuntimeIlcPackageTarget" Condition="'$(BuildingFrameworkLibrary)' != 'true' and '$(PublishAot)' == 'true'" DependsOnTargets="$(ImportRuntimeIlcPackageTargetDependsOn)" BeforeTargets="Publish">
+  <Target Name="ImportRuntimeIlcPackageTarget" Condition="'$(BuildingFrameworkLibrary)' != 'true' and '$(PublishAot)' == 'true'" DependsOnTargets="$(ImportRuntimeIlcPackageTargetDependsOn)">
     <Error Condition="'@(ResolvedILCompilerPack)' == ''" Text="The ResolvedILCompilerPack ItemGroup is required for target ImportRuntimeIlcPackageTarget" />
 
     <PropertyGroup>
diff --git a/src/coreclr/nativeaot/BuildIntegration/Microsoft.NETCore.Native.Publish.targets b/src/coreclr/nativeaot/BuildIntegration/Microsoft.NETCore.Native.Publish.targets
index 1776c7bf1d4ed5..255dd63ef53ed9 100644
--- a/src/coreclr/nativeaot/BuildIntegration/Microsoft.NETCore.Native.Publish.targets
+++ b/src/coreclr/nativeaot/BuildIntegration/Microsoft.NETCore.Native.Publish.targets
@@ -14,13 +14,21 @@
   </Target>
 
   <!--
-    This target hooks into the dotnet CLI publish pipeline. That pipeline has
-    a target called ComputeFilesToPublish which produces the ItemGroup
-    ResolvedFileToPublish. We modify this item group to control what gets
-    published after NativeAOT optimizes the application.
+    ============================================================
+                                        NativeCompile
+
+    Redefine the SDK's empty NativeCompile placeholder target to perform the full
+    NativeAOT compilation pipeline: ILC compilation, native linking, and updating
+    ResolvedFileToPublish to replace managed assemblies with the native binary.
+
+    The SDK typically sequences this target in the publish pipeline as:
+      ComputeResolvedFilesToPublishList -> ILLink (when RunILLink is true) -> NativeCompile -> ...
+
+    This gives us a clean, explicit position after trim configuration (_PrepareTrimConfiguration),
+    regardless of whether ILLink itself runs.
+    ============================================================
   -->
-  <Target Name="ComputeLinkedFilesToPublish"
-          AfterTargets="ComputeResolvedFilesToPublishList"
+  <Target Name="NativeCompile"
           DependsOnTargets="_ComputeAssembliesToCompileToNative;LinkNative">
 
     <ItemGroup>
@@ -60,6 +68,10 @@
     </ItemGroup>
   </Target>
 
+  <!-- Back-compat: keep ComputeLinkedFilesToPublish as an empty target for anything that
+       references it via BeforeTargets/AfterTargets. The work moved to NativeCompile. -->
+  <Target Name="ComputeLinkedFilesToPublish" />
+
   <!--
     Classify ResolvedFileToPublish for NativeAOT, then replace CoreCLR runtime pack
     files with DefaultFrameworkAssemblies (tagged PostprocessAssembly=true) so that
diff --git a/src/coreclr/nativeaot/BuildIntegration/Microsoft.NETCore.Native.targets b/src/coreclr/nativeaot/BuildIntegration/Microsoft.NETCore.Native.targets
index 87ec015589ce12..5a46ef07e238bb 100644
--- a/src/coreclr/nativeaot/BuildIntegration/Microsoft.NETCore.Native.targets
+++ b/src/coreclr/nativeaot/BuildIntegration/Microsoft.NETCore.Native.targets
@@ -119,7 +119,7 @@ The .NET Foundation licenses this file to you under the MIT license.
   </ItemDefinitionGroup>
 
   <!-- The properties below need to be defined only after we've found the correct runtime package reference -->
-  <Target Name="SetupProperties" DependsOnTargets="$(IlcSetupPropertiesDependsOn)" BeforeTargets="Publish">
+  <Target Name="SetupProperties" DependsOnTargets="$(IlcSetupPropertiesDependsOn)">
     <ItemGroup>
       <_NETCoreAppFrameworkReference Include="@(ResolvedFrameworkReference)" Condition="'%(ResolvedFrameworkReference.RuntimePackName)' == 'Microsoft.NETCore.App.Runtime.NativeAOT.$(RuntimeIdentifier)'" />
     </ItemGroup>
@@ -156,7 +156,7 @@ The .NET Foundation licenses this file to you under the MIT license.
     </ItemGroup>
   </Target>
 
-  <Target Name="ComputeIlcCompileInputs" DependsOnTargets="$(IlcDynamicBuildPropertyDependencies)" BeforeTargets="Publish">
+  <Target Name="ComputeIlcCompileInputs" DependsOnTargets="$(IlcDynamicBuildPropertyDependencies)">
     <ItemGroup>
       <ManagedBinary Condition="$(BuildingFrameworkLibrary) != 'true'" Include="@(IntermediateAssembly)" />
       <IlcCompileInput Include="@(ManagedBinary)" />
diff --git a/src/tests/Directory.Build.props b/src/tests/Directory.Build.props
index df43d981422b54..b6dce9ef455492 100644
--- a/src/tests/Directory.Build.props
+++ b/src/tests/Directory.Build.props
@@ -143,6 +143,7 @@
     <RunAnalyzers>false</RunAnalyzers>
     <EnableTrimAnalyzer>false</EnableTrimAnalyzer>
     <EnableAotAnalyzer>false</EnableAotAnalyzer>
+    <EnableSingleFileAnalyzer>false</EnableSingleFileAnalyzer>
     <GenerateAssemblyInfo>false</GenerateAssemblyInfo>
     <SkipSigning Condition="'$(CrossGen)' == 'true'">true</SkipSigning>
     <AssemblyKey>Test</AssemblyKey>
diff --git a/src/tests/Directory.Build.targets b/src/tests/Directory.Build.targets
index bd7093beb18339..c9a5138af52d8a 100644
--- a/src/tests/Directory.Build.targets
+++ b/src/tests/Directory.Build.targets
@@ -544,6 +544,12 @@
 
     <IlcTreatWarningsAsErrors>false</IlcTreatWarningsAsErrors>
 
+    <!-- Use the SDK's ILCompilerTargetsPath hook to import ILC targets in the correct order
+         (before ILLink), matching how the shipping SDK imports them. -->
+    <PublishAot>true</PublishAot>
+    <_IlcReferencedAsPackage>false</_IlcReferencedAsPackage>
+    <ILCompilerTargetsPath>$(CoreCLRBuildIntegrationDir)Microsoft.DotNet.ILCompiler.SingleEntry.targets</ILCompilerTargetsPath>
+
     <IlcToolsPath>$(CoreCLRCrossILCompilerDir)</IlcToolsPath>
     <IlcBuildTasksPath>$(CoreCLRILCompilerDir)netstandard/ILCompiler.Build.Tasks.dll</IlcBuildTasksPath>
     <IlcSdkPath>$(CoreCLRAotSdkDir)</IlcSdkPath>
@@ -575,7 +581,6 @@
 
   <Import Project="$(RepositoryEngineeringDir)nativeSanitizers.targets" Condition="'$(TestBuildMode)' == 'nativeaot'" />
 
-  <Import Project="$(CoreCLRBuildIntegrationDir)Microsoft.DotNet.ILCompiler.SingleEntry.targets" Condition="'$(TestBuildMode)' == 'nativeaot'" />
   <Import Project="$(RepoRoot)eng/liveILLink.targets" />
 
   <ItemGroup Condition="'$(TestBuildMode)' == 'nativeaot'">