diff --git a/src/coreclr/nativeaot/BuildIntegration/Microsoft.NETCore.Native.Publish.targets b/src/coreclr/nativeaot/BuildIntegration/Microsoft.NETCore.Native.Publish.targets
index c31ed57ee902da..6de6bf53f99454 100644
--- a/src/coreclr/nativeaot/BuildIntegration/Microsoft.NETCore.Native.Publish.targets
+++ b/src/coreclr/nativeaot/BuildIntegration/Microsoft.NETCore.Native.Publish.targets
@@ -2,9 +2,11 @@
 
   <Target Name="_ComputeIlcCompileInputs"
           BeforeTargets="ComputeIlcCompileInputs"
-          DependsOnTargets="$(IlcDynamicBuildPropertyDependencies)">
+          DependsOnTargets="$(IlcDynamicBuildPropertyDependencies);_ComputeAssembliesToCompileToNative;_PrepareTrimConfiguration">
+
     <ItemGroup>
-      <IlcReference Include="@(_ManagedResolvedAssembliesToPublish)" />
+      <_IlcManagedInputAssemblies Include="@(ResolvedFileToPublish)" Condition="'%(ResolvedFileToPublish.PostprocessAssembly)' == 'true'" />
+      <IlcReference Include="@(_IlcManagedInputAssemblies)" />
       <IlcSatelliteAssembly Include="@(_SatelliteAssembliesToPublish)" />
       <IlcSatelliteAssembly Include="@(IntermediateSatelliteAssembliesWithTargetPath)" />
     </ItemGroup>
@@ -14,14 +16,16 @@
     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.
+    published after NativeAOT optimizes the application. Hooks after ILLink,
+    which runs after ComputeResolvedFilesToPublishList, to ensure correct
+    ordering for scenarios that run both.
   -->
   <Target Name="ComputeLinkedFilesToPublish"
-          AfterTargets="ComputeResolvedFilesToPublishList"
+          AfterTargets="ILLink"
           DependsOnTargets="_ComputeAssembliesToCompileToNative;LinkNative">
 
     <ItemGroup>
-      <ResolvedFileToPublish Remove="@(_AssembliesToSkipPublish)" />
+      <ResolvedFileToPublish Remove="@(_IlcManagedInputAssemblies)" />
       <!-- dotnet CLI produces managed debug symbols, which we will replace with native symbols instead -->
       <ResolvedFileToPublish Remove="@(_DebugSymbolsIntermediatePath)" />
       <!-- replace apphost with binary we generated during native compilation -->
@@ -29,8 +33,6 @@
         <RelativePath>$(NativeBinaryPrefix)$(TargetName)$(NativeBinaryExt)</RelativePath>
         <CopyToPublishDirectory>PreserveNewest</CopyToPublishDirectory>
       </ResolvedFileToPublish>
-      <IntermediateAssembly Remove="@(IntermediateAssembly)" />
-      <IntermediateAssembly Include="$(NativeBinary)" />
     </ItemGroup>
 
     <PropertyGroup Condition="'$(CopyOutputSymbolsToPublishDirectory)' == 'true'">
@@ -60,13 +62,14 @@
   </Target>
 
   <!--
-    Filter the input publish file list selecting managed assemblies for compilation.
-    Also produces _AssembliesToSkipPublish which chops out things from the publish
-    pipeline we don't want to see in the output (native images, CoreCLR artifacts)
-    until we get a proper AOT NetCore app package.
+    Classify ResolvedFileToPublish for NativeAOT, then replace CoreCLR runtime pack
+    files with DefaultFrameworkAssemblies (tagged PostprocessAssembly=true) so that
+    trim metadata and ILC input selection operate on the correct set of assemblies.
   -->
   <UsingTask TaskName="ComputeManagedAssembliesToCompileToNative" AssemblyFile="$(IlcBuildTasksPath)" />
-  <Target Name="_ComputeAssembliesToCompileToNative" DependsOnTargets="$(IlcDynamicBuildPropertyDependencies);_ComputeAssembliesToPostprocessOnPublish">
+  <Target Name="_ComputeAssembliesToCompileToNative"
+          DependsOnTargets="$(IlcDynamicBuildPropertyDependencies);_ComputeAssembliesToPostprocessOnPublish"
+          BeforeTargets="_PrepareTrimConfiguration">
 
     <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. -->
@@ -104,11 +107,18 @@
       SdkAssemblies="@(PrivateSdkAssemblies)"
       FrameworkAssemblies="@(FrameworkAssemblies)">
 
-      <Output TaskParameter="ManagedAssemblies" ItemName="_ManagedResolvedAssembliesToPublish" />
       <Output TaskParameter="SatelliteAssemblies" ItemName="_SatelliteAssembliesToPublish" />
-      <Output TaskParameter="AssembliesToSkipPublish" ItemName="_AssembliesToSkipPublish" />
+      <Output TaskParameter="RuntimePackFilesToSkipPublish" ItemName="_RuntimePackFilesToSkipPublish" />
     </ComputeManagedAssembliesToCompileToNative>
 
+    <!-- Replace CoreCLR runtime pack with NativeAOT equivalents, tagged PostprocessAssembly=true. -->
+    <ItemGroup>
+      <ResolvedFileToPublish Remove="@(_RuntimePackFilesToSkipPublish)" />
+      <ResolvedFileToPublish Include="@(DefaultFrameworkAssemblies)">
+        <PostprocessAssembly>true</PostprocessAssembly>
+      </ResolvedFileToPublish>
+    </ItemGroup>
+
   </Target>
 
   <!-- Empty target to provide back-compat for other targets that run before/after CopyNativeBinary. -->
diff --git a/src/coreclr/nativeaot/BuildIntegration/Microsoft.NETCore.Native.targets b/src/coreclr/nativeaot/BuildIntegration/Microsoft.NETCore.Native.targets
index e758f681c3c0ee..33664c250d44fa 100644
--- a/src/coreclr/nativeaot/BuildIntegration/Microsoft.NETCore.Native.targets
+++ b/src/coreclr/nativeaot/BuildIntegration/Microsoft.NETCore.Native.targets
@@ -27,7 +27,7 @@ The .NET Foundation licenses this file to you under the MIT license.
     <ErrorOnDuplicatePublishOutputFiles>false</ErrorOnDuplicatePublishOutputFiles>
     <PublishTrimmed Condition="'$(PublishTrimmed)' == ''">true</PublishTrimmed>
     <IlcPgoOptimize Condition="'$(IlcPgoOptimize)' == '' and '$(OptimizationPreference)' == 'Speed'">true</IlcPgoOptimize>
-    <RunILLink>false</RunILLink>
+    <RunILLink Condition="'$(RunILLink)' == ''">false</RunILLink>
     <IlcTreatWarningsAsErrors Condition="'$(IlcTreatWarningsAsErrors)' == ''">$(TreatWarningsAsErrors)</IlcTreatWarningsAsErrors>
     <_IsiOSLikePlatform Condition="'$(_targetOS)' == 'maccatalyst' or $(_targetOS.StartsWith('ios')) or $(_targetOS.StartsWith('tvos'))">true</_IsiOSLikePlatform>
     <_IsApplePlatform Condition="'$(_targetOS)' == 'osx' or '$(_IsiOSLikePlatform)' == 'true'">true</_IsApplePlatform>
@@ -101,7 +101,6 @@ The .NET Foundation licenses this file to you under the MIT license.
     <IlcCompileDependsOn Condition="'$(BuildingFrameworkLibrary)' != 'true'">Compile;ComputeIlcCompileInputs</IlcCompileDependsOn>
     <IlcCompileDependsOn Condition="'$(IlcMultiModule)' == 'true' and '$(BuildingFrameworkLibrary)' != 'true'">$(IlcCompileDependsOn);BuildFrameworkLib</IlcCompileDependsOn>
     <IlcCompileDependsOn>$(IlcCompileDependsOn);SetupOSSpecificProps</IlcCompileDependsOn>
-    <IlcCompileDependsOn>$(IlcCompileDependsOn);PrepareForILLink</IlcCompileDependsOn>
   </PropertyGroup>
 
   <ItemGroup Condition="$(IlcSystemModule) == ''">
@@ -119,15 +118,6 @@ The .NET Foundation licenses this file to you under the MIT license.
     </ManagedBinary>
   </ItemDefinitionGroup>
 
-  <Target Name="_ComputeManagedAssemblyForILLink"
-          AfterTargets="_ComputeManagedAssemblyToLink"
-          Condition="'$(NativeCompilationDuringPublish)' == 'true'">
-    <ItemGroup>
-      <ManagedAssemblyToLink Remove="@(ManagedAssemblyToLink)" />
-      <ManagedAssemblyToLink Include="@(DefaultFrameworkAssemblies);@(_ManagedResolvedAssembliesToPublish);@(ManagedBinary)" />
-    </ItemGroup>
-  </Target>
-
   <!-- The properties below need to be defined only after we've found the correct runtime package reference -->
   <Target Name="SetupProperties" DependsOnTargets="$(IlcSetupPropertiesDependsOn)" BeforeTargets="Publish">
     <ItemGroup>
@@ -170,7 +160,6 @@ The .NET Foundation licenses this file to you under the MIT license.
     <ItemGroup>
       <ManagedBinary Condition="$(BuildingFrameworkLibrary) != 'true'" Include="@(IntermediateAssembly)" />
       <IlcCompileInput Include="@(ManagedBinary)" />
-      <IlcReference Include="@(DefaultFrameworkAssemblies)" />
     </ItemGroup>
   </Target>
 
@@ -200,13 +189,12 @@ The .NET Foundation licenses this file to you under the MIT license.
       DependsOnTargets="$(IlcCompileDependsOn)">
 
     <ItemGroup>
-      <!-- Grab the raw ItemGroup that ILLinker accepts in two form: as file names, and as assembly names -->
       <_IlcRootedAssembliesRaw Include="@(TrimmerRootAssembly)" Condition="%(TrimmerRootAssembly.RootMode) != 'EntryPoint'" />
-      <_IlcRootedAssembliesRaw Include="@(ManagedAssemblyToLink)" Condition="%(ManagedAssemblyToLink.TrimMode) == 'copy'" />
-      <_IlcConditionallyRootedAssembliesRaw Include="@(ManagedAssemblyToLink)" Condition="%(ManagedAssemblyToLink.TrimMode) == 'copyused'" />
-      <_IlcTrimmedAssembliesRaw Include="@(ManagedAssemblyToLink)" Condition="%(ManagedAssemblyToLink.TrimMode) == 'link'" />
-      <_IlcSingleWarnAssembliesRaw Include="@(ManagedAssemblyToLink)" Condition="%(ManagedAssemblyToLink.TrimmerSingleWarn) == 'true'" />
-      <_IlcNoSingleWarnAssembliesRaw Include="@(ManagedAssemblyToLink)" Condition="%(ManagedAssemblyToLink.TrimmerSingleWarn) == 'false'" />
+      <_IlcRootedAssembliesRaw Include="@(_IlcManagedInputAssemblies)" Condition="%(_IlcManagedInputAssemblies.TrimMode) == 'copy'" />
+      <_IlcConditionallyRootedAssembliesRaw Include="@(_IlcManagedInputAssemblies)" Condition="%(_IlcManagedInputAssemblies.TrimMode) == 'copyused'" />
+      <_IlcTrimmedAssembliesRaw Include="@(_IlcManagedInputAssemblies)" Condition="%(_IlcManagedInputAssemblies.TrimMode) == 'link'" />
+      <_IlcSingleWarnAssembliesRaw Include="@(_IlcManagedInputAssemblies)" Condition="%(_IlcManagedInputAssemblies.TrimmerSingleWarn) == 'true'" />
+      <_IlcNoSingleWarnAssembliesRaw Include="@(_IlcManagedInputAssemblies)" Condition="%(_IlcManagedInputAssemblies.TrimmerSingleWarn) == 'false'" />
 
       <!-- Now process the raw ItemGroup into the form that ILC accepts: assembly names only -->
       <!-- Use the logic that ILLinker uses: if the file exists, this is a file name. Otherwise it's an assembly name -->
diff --git a/src/coreclr/tools/aot/ILCompiler.Build.Tasks/ComputeManagedAssembliesToCompileToNative.cs b/src/coreclr/tools/aot/ILCompiler.Build.Tasks/ComputeManagedAssembliesToCompileToNative.cs
index 6ed14b4e3e25c4..19d435e2303422 100644
--- a/src/coreclr/tools/aot/ILCompiler.Build.Tasks/ComputeManagedAssembliesToCompileToNative.cs
+++ b/src/coreclr/tools/aot/ILCompiler.Build.Tasks/ComputeManagedAssembliesToCompileToNative.cs
@@ -74,13 +74,6 @@ public string DotNetHostPolicyLibraryName
             set;
         }
 
-        [Output]
-        public ITaskItem[] ManagedAssemblies
-        {
-            get;
-            set;
-        }
-
         [Output]
         public ITaskItem[] SatelliteAssemblies
         {
@@ -88,8 +81,12 @@ public ITaskItem[] SatelliteAssemblies
             set;
         }
 
+        /// <summary>
+        /// CoreCLR runtime pack files (apphost, native assets, managed assemblies replaced by NativeAOT equivalents)
+        /// that should be removed from the publish output and replaced with NativeAOT runtime pack assemblies.
+        /// </summary>
         [Output]
-        public ITaskItem[] AssembliesToSkipPublish
+        public ITaskItem[] RuntimePackFilesToSkipPublish
         {
             get;
             set;
@@ -97,8 +94,7 @@ public ITaskItem[] AssembliesToSkipPublish
 
         public override bool Execute()
         {
-            var list = new List<ITaskItem>();
-            var assembliesToSkipPublish = new List<ITaskItem>();
+            var runtimePackFilesToSkipPublish = new List<ITaskItem>();
             var satelliteAssemblies = new List<ITaskItem>();
             var nativeAotFrameworkAssembliesToUse = new Dictionary<string, ITaskItem>();
 
@@ -126,7 +122,7 @@ public override bool Execute()
                 // Skip the native apphost (whose name ends up colliding with the native output binary) and supporting libraries
                 if (itemSpec.EndsWith(DotNetAppHostExecutableName, StringComparison.OrdinalIgnoreCase) || itemSpec.Contains(DotNetHostFxrLibraryName) || itemSpec.Contains(DotNetHostPolicyLibraryName))
                 {
-                    assembliesToSkipPublish.Add(taskItem);
+                    runtimePackFilesToSkipPublish.Add(taskItem);
                     continue;
                 }
 
@@ -135,7 +131,7 @@ public override bool Execute()
                     && !assemblyFileName.EndsWith(".dex", StringComparison.OrdinalIgnoreCase))
                 {
                     // Skip the native components of the runtime pack, we don't need them for NativeAOT.
-                    assembliesToSkipPublish.Add(taskItem);
+                    runtimePackFilesToSkipPublish.Add(taskItem);
                     continue;
                 }
 
@@ -148,8 +144,10 @@ public override bool Execute()
                     if (!isFromRuntimePack)
                     {
                         // The assembly was overridden by an OOB package through standard .NET SDK conflict resolution.
-                        // Use that version instead of swapping to the NativeAOT one.
-                        list.Add(taskItem);
+                        // Don't swap to the NativeAOT version; the user's version stays in
+                        // ResolvedFileToPublish and will be picked up as an ILC input via
+                        // its PostprocessAssembly=true metadata.
+                        continue;
                     }
                     else if (assemblyFileName == "System.Private.CoreLib.dll" && GetFileVersion(itemSpec).CompareTo(GetFileVersion(frameworkItem.ItemSpec)) > 0)
                     {
@@ -158,7 +156,7 @@ public override bool Execute()
                         Log.LogError($"Overriding System.Private.CoreLib.dll with a newer version is not supported. Attempted to use {itemSpec} instead of {frameworkItem.ItemSpec}.");
                     }
 
-                    assembliesToSkipPublish.Add(taskItem);
+                    runtimePackFilesToSkipPublish.Add(taskItem);
                     continue;
                 }
 
@@ -170,9 +168,8 @@ public override bool Execute()
                     continue;
                 }
 
-                // For all other files, check if they are managed assemblies.
-                // If they're managed, skip publishing them and categorize them correctly as inputs to ILC.
-                // If they're not managed assemblies, then they're native dependencies. Allow them to be published.
+                // Check if this is a satellite assembly by reading its culture metadata.
+                // Non-managed files are silently skipped as a safety measure.
                 try
                 {
                     using (FileStream moduleStream = File.OpenRead(itemSpec))
@@ -185,14 +182,7 @@ public override bool Execute()
                             {
                                 string culture = moduleMetadataReader.GetString(moduleMetadataReader.GetAssemblyDefinition().Culture);
 
-                                assembliesToSkipPublish.Add(taskItem);
-
-                                // Split satellite assemblies from normal assemblies
-                                if (culture == "" || culture.Equals("neutral", StringComparison.OrdinalIgnoreCase))
-                                {
-                                    list.Add(taskItem);
-                                }
-                                else
+                                if (culture != "" && !culture.Equals("neutral", StringComparison.OrdinalIgnoreCase))
                                 {
                                     satelliteAssemblies.Add(taskItem);
                                 }
@@ -205,8 +195,7 @@ public override bool Execute()
                 }
             }
 
-            ManagedAssemblies = list.ToArray();
-            AssembliesToSkipPublish = assembliesToSkipPublish.ToArray();
+            RuntimePackFilesToSkipPublish = runtimePackFilesToSkipPublish.ToArray();
             SatelliteAssemblies = satelliteAssemblies.ToArray();
 
             return true;
diff --git a/src/tools/illink/src/ILLink.Tasks/build/Microsoft.NET.ILLink.targets b/src/tools/illink/src/ILLink.Tasks/build/Microsoft.NET.ILLink.targets
index 16198390f88f7b..7812d9f85bd45e 100644
--- a/src/tools/illink/src/ILLink.Tasks/build/Microsoft.NET.ILLink.targets
+++ b/src/tools/illink/src/ILLink.Tasks/build/Microsoft.NET.ILLink.targets
@@ -193,11 +193,71 @@ Copyright (c) .NET Foundation. All rights reserved.
 
   </Target>
 
+  <!--
+    ============================================================
+                     _PrepareTrimConfiguration
+
+    Set up shared trim configuration properties and metadata on ResolvedFileToPublish.
+    This target is shared between ILLink and ILC (NativeAOT). It sets default values for
+    trim-related properties (TrimMode, TrimmerSingleWarn), populates TrimmerRootAssembly
+    and _TrimmerFeatureSettings, and applies TrimmerSingleWarn metadata to
+    ResolvedFileToPublish items for the intermediate assembly and project references.
+
+    Consumers that need trim metadata on ResolvedFileToPublish should depend on this target.
+    Metadata set here flows to ManagedAssemblyToLink via _ComputeManagedAssemblyToLink (which
+    depends on this target), since ComputeManagedAssemblies preserves metadata from its inputs.
+   -->
+   <Target Name="_PrepareTrimConfiguration"
+           DependsOnTargets="_ComputeAssembliesToPostprocessOnPublish">
+
+    <!-- Set up TrimMode. -->
+    <PropertyGroup>
+      <TrimMode Condition="'$(TrimMode)' == ''">full</TrimMode>
+    </PropertyGroup>
+
+    <PropertyGroup>
+      <TrimmerSingleWarn Condition=" '$(TrimmerSingleWarn)' == '' ">true</TrimmerSingleWarn>
+    </PropertyGroup>
+
+    <!-- Root the main assembly entry point. -->
+    <ItemGroup>
+      <TrimmerRootAssembly Include="@(IntermediateAssembly)" RootMode="EntryPoint" />
+    </ItemGroup>
+
+    <ItemGroup>
+      <!-- Don't collapse to a single warning for the intermediate assembly.
+           This sets metadata on the items in ResolvedFileToPublish that came from IntermediateAssembly. -->
+      <!-- Find ResolvedFileToPublish _except_ IntermediateAssembly -->
+      <__SingleWarnIntermediateAssembly Include="@(ResolvedFileToPublish)" />
+      <__SingleWarnIntermediateAssembly Remove="@(IntermediateAssembly)" />
+      <!-- Subtract these from ResolvedFileToPublish, to get the intersection. -->
+      <_SingleWarnIntermediateAssembly Include="@(ResolvedFileToPublish)" />
+      <_SingleWarnIntermediateAssembly Remove="@(__SingleWarnIntermediateAssembly)" />
+      <!-- Set metadata on the intersection. -->
+      <_SingleWarnIntermediateAssembly>
+        <TrimmerSingleWarn Condition=" '%(_SingleWarnIntermediateAssembly.TrimmerSingleWarn)' == '' ">false</TrimmerSingleWarn>
+      </_SingleWarnIntermediateAssembly>
+      <!-- Replace these items in ResolvedFileToPublish. -->
+      <ResolvedFileToPublish Remove="@(_SingleWarnIntermediateAssembly)" />
+      <ResolvedFileToPublish Include="@(_SingleWarnIntermediateAssembly)" />
+
+      <!-- Don't collapse to a single warning for project references -->
+      <ResolvedFileToPublish Condition=" '%(ResolvedFileToPublish.ProjectReferenceOriginalItemSpec)' != '' ">
+        <TrimmerSingleWarn Condition=" '%(ResolvedFileToPublish.TrimmerSingleWarn)' == '' ">false</TrimmerSingleWarn>
+      </ResolvedFileToPublish>
+    </ItemGroup>
+
+    <ItemGroup>
+      <_TrimmerFeatureSettings Include="@(RuntimeHostConfigurationOption)" Condition="'%(RuntimeHostConfigurationOption.Trim)' == 'true'" />
+    </ItemGroup>
+
+   </Target>
+
   <!--
     ============================================================
                      PrepareForILLink
 
-    Set up the default options and inputs to ILLink. Other targets are expected to hook into
+    Set up the ILLink-specific options and inputs. Other targets are expected to hook into
     this extension point via BeforeTargets/AfterTargets to opt assemblies into or out of trimming
     using global ILLink options, or per-assembly IsTrimmable and TrimMode metadata.
 
@@ -236,14 +296,8 @@ Copyright (c) .NET Foundation. All rights reserved.
       <_ExtraTrimmerArgs>$(_ExtraTrimmerArgs) --link-attributes "@(_ILLinkSuppressions->'%(Identity)', '" --link-attributes "')"</_ExtraTrimmerArgs>
     </PropertyGroup>
 
-    <!-- Set up TrimMode. -->
-    <PropertyGroup>
-      <TrimMode Condition="'$(TrimMode)' == ''">full</TrimMode>
-    </PropertyGroup>
-
     <PropertyGroup>
       <ILLinkTreatWarningsAsErrors Condition=" '$(ILLinkTreatWarningsAsErrors)' == '' ">$(TreatWarningsAsErrors)</ILLinkTreatWarningsAsErrors>
-      <TrimmerSingleWarn Condition=" '$(TrimmerSingleWarn)' == '' ">true</TrimmerSingleWarn>
     </PropertyGroup>
 
     <!-- Set a default value for TrimmerRemoveSymbols unless set explicitly. -->
@@ -281,38 +335,6 @@ Copyright (c) .NET Foundation. All rights reserved.
       <ManagedAssemblyToLink Include="@(_TrimmableManagedAssemblyToLink)" IsTrimmable="true" />
     </ItemGroup>
 
-    <!-- Root the main assembly entry point. -->
-    <ItemGroup>
-      <TrimmerRootAssembly Include="@(IntermediateAssembly)" RootMode="EntryPoint" />
-    </ItemGroup>
-
-    <ItemGroup>
-      <!-- Don't collapse to a single warning for the intermediate assembly.
-           This just sets metadata on the items in ManagedAssemblyToLink that came from IntermediateAssembly. -->
-      <!-- Find ManagedAssemblyToLink _except_ IntermediateAssembly -->
-      <__SingleWarnIntermediateAssembly Include="@(ManagedAssemblyToLink)" />
-      <__SingleWarnIntermediateAssembly Remove="@(IntermediateAssembly)" />
-      <!-- Subtract these from ManagedAssemblyToLink, to get the intersection. -->
-      <_SingleWarnIntermediateAssembly Include="@(ManagedAssemblyToLink)" />
-      <_SingleWarnIntermediateAssembly Remove="@(__SingleWarnIntermediateAssembly)" />
-      <!-- Set metadata on the intersection. -->
-      <_SingleWarnIntermediateAssembly>
-        <TrimmerSingleWarn Condition=" '%(_SingleWarnIntermediateAssembly.TrimmerSingleWarn)' == '' ">false</TrimmerSingleWarn>
-      </_SingleWarnIntermediateAssembly>
-      <!-- Replace these items in ManagedAssemblyToLink. -->
-      <ManagedAssemblyToLink Remove="@(_SingleWarnIntermediateAssembly)" />
-      <ManagedAssemblyToLink Include="@(_SingleWarnIntermediateAssembly)" />
-
-      <!-- Don't collapse to a single warning for project references -->
-      <ManagedAssemblyToLink Condition=" '%(ManagedAssemblyToLink.ProjectReferenceOriginalItemSpec)' != '' ">
-        <TrimmerSingleWarn Condition=" '%(ManagedAssemblyToLink.TrimmerSingleWarn)' == '' ">false</TrimmerSingleWarn>
-      </ManagedAssemblyToLink>
-    </ItemGroup>
-
-    <ItemGroup>
-      <_TrimmerFeatureSettings Include="@(RuntimeHostConfigurationOption)" Condition="'%(RuntimeHostConfigurationOption.Trim)' == 'true'" />
-    </ItemGroup>
-
    </Target>
 
   <!--
@@ -323,7 +345,7 @@ Copyright (c) .NET Foundation. All rights reserved.
     ============================================================
     -->
   <UsingTask TaskName="ComputeManagedAssemblies" AssemblyFile="$(ILLinkTasksAssembly)" Condition="'$(ILLinkTasksAssembly)' != ''" TaskFactory="TaskHostFactory" />
-  <Target Name="_ComputeManagedAssemblyToLink" DependsOnTargets="_ComputeAssembliesToPostprocessOnPublish">
+  <Target Name="_ComputeManagedAssemblyToLink" DependsOnTargets="_PrepareTrimConfiguration">
 
     <!-- NB: There should not be non-managed assemblies in this list, but we still give the ILLink a chance to
          further refine this list. It currently drops C++/CLI assemblies in ComputeManageAssemblies. -->