diff --git a/src/coreclr/nativeaot/BuildIntegration/Microsoft.NETCore.Native.targets b/src/coreclr/nativeaot/BuildIntegration/Microsoft.NETCore.Native.targets
index 45589a0fc993d7..4d62e2f0516089 100644
--- a/src/coreclr/nativeaot/BuildIntegration/Microsoft.NETCore.Native.targets
+++ b/src/coreclr/nativeaot/BuildIntegration/Microsoft.NETCore.Native.targets
@@ -218,16 +218,17 @@ The .NET Foundation licenses this file to you under the MIT license.
 
       <!-- 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 -->
-      <_IlcRootedAssemblies Include="@(_IlcRootedAssembliesRaw->'%(Filename)')" Condition="Exists('%(Identity)')" />
-      <_IlcRootedAssemblies Include="@(_IlcRootedAssembliesRaw)" Condition="!Exists('%(Identity)')" />
-      <_IlcConditionallyRootedAssemblies Include="@(_IlcConditionallyRootedAssembliesRaw->'%(Filename)')" Condition="Exists('%(Identity)')" />
-      <_IlcConditionallyRootedAssemblies Include="@(_IlcConditionallyRootedAssembliesRaw)" Condition="!Exists('%(Identity)')" />
-      <_IlcTrimmedAssemblies Include="@(_IlcTrimmedAssembliesRaw->'%(Filename)')" Condition="Exists('%(Identity)')" />
-      <_IlcTrimmedAssemblies Include="@(_IlcTrimmedAssembliesRaw)" Condition="!Exists('%(Identity)')" />
-      <_IlcSingleWarnAssemblies Include="@(_IlcSingleWarnAssembliesRaw->'%(Filename)')" Condition="Exists('%(Identity)')" />
-      <_IlcSingleWarnAssemblies Include="@(_IlcSingleWarnAssembliesRaw)" Condition="!Exists('%(Identity)')" />
-      <_IlcNoSingleWarnAssemblies Include="@(_IlcNoSingleWarnAssembliesRaw->'%(Filename)')" Condition="Exists('%(Identity)')" />
-      <_IlcNoSingleWarnAssemblies Include="@(_IlcNoSingleWarnAssembliesRaw)" Condition="!Exists('%(Identity)')" />
+      <!-- Use System.IO.File.Exists() to avoid directories-->
+      <_IlcRootedAssemblies Include="@(_IlcRootedAssembliesRaw->'%(Filename)')" Condition="$([System.IO.File]::Exists('%(Identity)'))" />
+      <_IlcRootedAssemblies Include="@(_IlcRootedAssembliesRaw)" Condition="!$([System.IO.File]::Exists('%(Identity)'))" />
+      <_IlcConditionallyRootedAssemblies Include="@(_IlcConditionallyRootedAssembliesRaw->'%(Filename)')" Condition="$([System.IO.File]::Exists('%(Identity)'))" />
+      <_IlcConditionallyRootedAssemblies Include="@(_IlcConditionallyRootedAssembliesRaw)" Condition="!$([System.IO.File]::Exists('%(Identity)'))" />
+      <_IlcTrimmedAssemblies Include="@(_IlcTrimmedAssembliesRaw->'%(Filename)')" Condition="$([System.IO.File]::Exists('%(Identity)'))" />
+      <_IlcTrimmedAssemblies Include="@(_IlcTrimmedAssembliesRaw)" Condition="!$([System.IO.File]::Exists('%(Identity)'))" />
+      <_IlcSingleWarnAssemblies Include="@(_IlcSingleWarnAssembliesRaw->'%(Filename)')" Condition="$([System.IO.File]::Exists('%(Identity)'))" />
+      <_IlcSingleWarnAssemblies Include="@(_IlcSingleWarnAssembliesRaw)" Condition="!$([System.IO.File]::Exists('%(Identity)'))" />
+      <_IlcNoSingleWarnAssemblies Include="@(_IlcNoSingleWarnAssembliesRaw->'%(Filename)')" Condition="$([System.IO.File]::Exists('%(Identity)'))" />
+      <_IlcNoSingleWarnAssemblies Include="@(_IlcNoSingleWarnAssembliesRaw)" Condition="!$([System.IO.File]::Exists('%(Identity)'))" />
     </ItemGroup>
 
     <ItemGroup>