diff --git a/tools/ExtensionsMetadataGenerator/src/ExtensionsMetadataGenerator/BuildTasks/RemoveRuntimeDependencies.cs b/tools/ExtensionsMetadataGenerator/src/ExtensionsMetadataGenerator/BuildTasks/RemoveRuntimeDependencies.cs
index 334d332a7f..69bd144ed2 100644
--- a/tools/ExtensionsMetadataGenerator/src/ExtensionsMetadataGenerator/BuildTasks/RemoveRuntimeDependencies.cs
+++ b/tools/ExtensionsMetadataGenerator/src/ExtensionsMetadataGenerator/BuildTasks/RemoveRuntimeDependencies.cs
@@ -21,8 +21,17 @@ public class RemoveRuntimeDependencies : Task
         [Required]
         public string OutputPath { get; set; }
 
+        [Required]
+        public ITaskItem[] IgnoreFiles { get; set; }
+
         public override bool Execute()
         {
+            HashSet<string> ignoreFilesSet = new HashSet<string>();
+            foreach (ITaskItem item in IgnoreFiles)
+            {
+                ignoreFilesSet.Add(item.ItemSpec);
+            }
+
             Assembly assembly = typeof(RemoveRuntimeDependencies).Assembly;
             using (Stream resource = assembly.GetManifestResourceStream(assembly.GetName().Name + ".runtimeassemblies.txt"))
             using (var reader = new StreamReader(resource))
@@ -32,7 +41,7 @@ public override bool Execute()
                 {
                     string fileName = Path.Combine(OutputPath, assemblyName);
 
-                    if (File.Exists(fileName))
+                    if (File.Exists(fileName) && !ignoreFilesSet.Contains(assemblyName))
                     {
                         File.Delete(fileName);
                     }
@@ -44,4 +53,4 @@ public override bool Execute()
             return true;
         }
     }
-}
+}
\ No newline at end of file
diff --git a/tools/ExtensionsMetadataGenerator/src/ExtensionsMetadataGenerator/Targets/Microsoft.Azure.WebJobs.Script.ExtensionsMetadataGenerator.targets b/tools/ExtensionsMetadataGenerator/src/ExtensionsMetadataGenerator/Targets/Microsoft.Azure.WebJobs.Script.ExtensionsMetadataGenerator.targets
index 30c7bbb658..b527f698b4 100644
--- a/tools/ExtensionsMetadataGenerator/src/ExtensionsMetadataGenerator/Targets/Microsoft.Azure.WebJobs.Script.ExtensionsMetadataGenerator.targets
+++ b/tools/ExtensionsMetadataGenerator/src/ExtensionsMetadataGenerator/Targets/Microsoft.Azure.WebJobs.Script.ExtensionsMetadataGenerator.targets
@@ -21,11 +21,11 @@
              AssemblyFile="$(_FunctionsExtensionsTaskAssemblyFullPath)"/>
   
   <Target Name="_FunctionsBuildCleanOutput" AfterTargets="_GenerateFunctionsExtensionsMetadataPostBuild" Condition="$(_FunctionsSkipCleanOutput) != 'true'" >
-    <RemoveRuntimeDependencies OutputPath="$(TargetDir)bin"/>
+    <RemoveRuntimeDependencies OutputPath="$(TargetDir)bin" IgnoreFiles="@(FunctionsPreservedDependencies)"/>
   </Target>
 
   <Target Name="_FunctionsPublishCleanOutput" AfterTargets="_GenerateFunctionsExtensionsMetadataPostPublish" Condition="$(_FunctionsSkipCleanOutput) != 'true'" >
-    <RemoveRuntimeDependencies OutputPath="$(PublishDir)bin"/>
+    <RemoveRuntimeDependencies OutputPath="$(PublishDir)bin" IgnoreFiles="@(FunctionsPreservedDependencies)"/>
   </Target>
   
   <UsingTask TaskName="GenerateFunctionsExtensionsMetadata"