diff --git a/eng/Subsets.props b/eng/Subsets.props
index aa4da501a51acc..45dd4d7a2c0058 100644
--- a/eng/Subsets.props
+++ b/eng/Subsets.props
@@ -440,9 +440,12 @@
     <ProjectToBuild Include="$(CoreClrProjectRoot)tools\aot\ILCompiler\ILCompiler.csproj" Condition="'$(NativeAotSupported)' == 'true' and '$(StageOneBuild)' != 'true'" Category="clr" />
     <ProjectToBuild Include="$(CoreClrProjectRoot)tools\aot\crossgen2\crossgen2.csproj" Condition="'$(NativeAotSupported)' == 'true' and '$(StageOneBuild)' != 'true'" Category="clr" />
 
-    <!-- Always build the in-build variants of these tools. They run on the host machine, which we always have LKG packs for. -->
-    <ProjectToBuild Include="$(CoreClrProjectRoot)tools\aot\ILCompiler\ILCompiler_inbuild.csproj" Category="clr" />
-    <ProjectToBuild Include="$(CoreClrProjectRoot)tools\aot\crossgen2\crossgen2_inbuild.csproj" Category="clr" />
+    <!--
+      Always build the in-build variants of these tools. They run on the host machine, which we always have LKG packs for.
+      For two-stage builds, we omit this step during stage2 since stage1 covers it.
+    -->
+    <ProjectToBuild Include="$(CoreClrProjectRoot)tools\aot\ILCompiler\ILCompiler_inbuild.csproj" Category="clr" Condition="'$(StageTwoBuild)' != 'true'" />
+    <ProjectToBuild Include="$(CoreClrProjectRoot)tools\aot\crossgen2\crossgen2_inbuild.csproj" Category="clr" Condition="'$(StageTwoBuild)' != 'true'" />
 
     <ProjectToBuild Condition="'$(TargetOS)' == 'windows' or ('$(TargetOS)' == 'linux' and ('$(TargetArchitecture)' == 'x64' or '$(TargetArchitecture)' == 'arm64')) or '$(TargetOS)' == 'osx'" Include="$(CoreClrProjectRoot)tools\SuperFileCheck\SuperFileCheck.csproj" Category="clr" />