diff --git a/src/Tasks/Microsoft.NET.Build.Tasks/targets/Microsoft.NET.ILLink.targets b/src/Tasks/Microsoft.NET.Build.Tasks/targets/Microsoft.NET.ILLink.targets
index bf6973b09d45..5bc6ef8145be 100644
--- a/src/Tasks/Microsoft.NET.Build.Tasks/targets/Microsoft.NET.ILLink.targets
+++ b/src/Tasks/Microsoft.NET.Build.Tasks/targets/Microsoft.NET.ILLink.targets
@@ -18,15 +18,8 @@ Copyright (c) .NET Foundation. All rights reserved.
     <IntermediateLinkDir Condition=" !HasTrailingSlash('$(IntermediateLinkDir)') ">$(IntermediateLinkDir)\</IntermediateLinkDir>
     <!-- Used to enable incremental build for the linker target. -->
     <_LinkSemaphore>$(IntermediateOutputPath)Link.semaphore</_LinkSemaphore>
-    <!-- Disable old deps file generation logic until
-         https://github.com/dotnet/sdk/issues/3098 is fixed. -->
-    <DepsFileGenerationMode>new</DepsFileGenerationMode>
   </PropertyGroup>
 
-  <ItemGroup>
-    <TrimmerRootDescriptors Include="$(TrimmerRootDescriptors)" />
-  </ItemGroup>
-
   <!--
     ============================================================
                      _ILLink
@@ -77,16 +70,16 @@ Copyright (c) .NET Foundation. All rights reserved.
    <UsingTask TaskName="ILLink" AssemblyFile="$(ILLinkTasksAssembly)" />
    <Target Name="_RunILLink"
            DependsOnTargets="_ComputeManagedAssembliesToLink"
-           Inputs="$(MSBuildAllProjects);@(_ManagedAssembliesToLink);@(TrimmerRootDescriptors);@(ReferencePath)"
+           Inputs="$(MSBuildAllProjects);@(_ManagedAssembliesToLink);@(TrimmerRootDescriptor);@(ReferencePath)"
            Outputs="$(_LinkSemaphore)">
 
      <Delete Files="@(_LinkedResolvedFileToPublishCandidates)" />
      <ILLink AssemblyPaths="@(_ManagedAssembliesToLink)"
              ReferenceAssemblyPaths="@(ReferencePath)"
              RootAssemblyNames="@(IntermediateAssembly->'%(Filename)')"
-             RootDescriptorFiles="@(TrimmerRootDescriptors)"
+             RootDescriptorFiles="@(TrimmerRootDescriptor)"
              OutputDirectory="$(IntermediateLinkDir)"
-             ExtraArgs="$(_ExtraTrimmerArgs) --skip-unresolved true" />
+             ExtraArgs="-u copyused -c copyused -l none --skip-unresolved true $(_ExtraTrimmerArgs)" />
 
      <Touch Files="$(_LinkSemaphore)" AlwaysCreate="true" />
 
diff --git a/src/Tests/Microsoft.NET.Publish.Tests/GivenThatWeWantToRunILLink.cs b/src/Tests/Microsoft.NET.Publish.Tests/GivenThatWeWantToRunILLink.cs
index add279e0a81e..442685886cdc 100644
--- a/src/Tests/Microsoft.NET.Publish.Tests/GivenThatWeWantToRunILLink.cs
+++ b/src/Tests/Microsoft.NET.Publish.Tests/GivenThatWeWantToRunILLink.cs
@@ -1,6 +1,7 @@
 using System;
 using System.IO;
 using System.Linq;
+using System.Xml.Linq;
 using System.Reflection.Metadata;
 using System.Reflection.PortableExecutable;
 using FluentAssertions;
@@ -103,11 +104,19 @@ public void ILLink_accepts_root_descriptor(string targetFramework)
 
             var testProject = CreateTestProjectForILLinkTesting(targetFramework, projectName, referenceProjectName);
             var testAsset = _testAssetsManager.CreateTestProject(testProject)
+                .WithProjectChanges(project => AddRootDescriptor(project, $"{referenceProjectName}.xml"))
                 .Restore(Log, testProject.Name, args: $"/p:RuntimeIdentifier={rid}");
 
             var publishCommand = new PublishCommand(Log, Path.Combine(testAsset.TestRoot, testProject.Name));
+            // Inject extra arguments to prevent the linker from
+            // keeping the entire referenceProject assembly. The
+            // linker by default runs in a conservative mode that
+            // keeps all used assemblies, but in this case we want to
+            // check whether the root descriptor actually roots only
+            // the specified method.
+            var extraArgs = $"-p link {referenceProjectName}";
             publishCommand.Execute($"/p:RuntimeIdentifier={rid}", $"/p:SelfContained=true", "/p:PublishTrimmed=true",
-                                   $"/p:TrimmerRootDescriptors={referenceProjectName}.xml").Should().Pass();
+                                   $"/p:_ExtraTrimmerArgs={extraArgs}", "/v:n").Should().Pass();
 
             var publishDirectory = publishCommand.GetOutputDirectory(targetFramework: targetFramework, runtimeIdentifier: rid).FullName;
             var publishedDll = Path.Combine(publishDirectory, $"{projectName}.dll");
@@ -161,6 +170,7 @@ public void ILLink_does_not_include_leftover_artifacts_on_second_run(string targ
 
             var testProject = CreateTestProjectForILLinkTesting(targetFramework, projectName, referenceProjectName);
             var testAsset = _testAssetsManager.CreateTestProject(testProject)
+                .WithProjectChanges(project => AddRootDescriptor(project, $"{referenceProjectName}.xml"))
                 .Restore(Log, testProject.Name, args: $"/p:RuntimeIdentifier={rid}");
 
             var publishCommand = new PublishCommand(Log, Path.Combine(testAsset.TestRoot, testProject.Name));
@@ -172,8 +182,9 @@ public void ILLink_does_not_include_leftover_artifacts_on_second_run(string targ
             var linkSemaphore = Path.Combine(intermediateDirectory, "Link.semaphore");
 
             // Link, keeping classlib
-            publishCommand.Execute($"/p:RuntimeIdentifier={rid}", $"/p:SelfContained=true", "/p:PublishTrimmed=true",
-                                   $"/p:TrimmerRootDescriptors={referenceProjectName}.xml").Should().Pass();
+            publishCommand.Execute($"/p:RuntimeIdentifier={rid}", $"/p:SelfContained=true", "/p:PublishTrimmed=true").Should().Pass();
+            DateTime semaphoreFirstModifiedTime = File.GetLastWriteTimeUtc(linkSemaphore);
+
             var publishedDllKeptFirstTimeOnly = Path.Combine(publishDirectory, $"{referenceProjectName}.dll");
             var linkedDllKeptFirstTimeOnly = Path.Combine(linkedDirectory, $"{referenceProjectName}.dll");
             File.Exists(linkedDllKeptFirstTimeOnly).Should().BeTrue();
@@ -182,12 +193,18 @@ public void ILLink_does_not_include_leftover_artifacts_on_second_run(string targ
             // Delete kept dll from publish output (works around lack of incremental publish)
             File.Delete(publishedDllKeptFirstTimeOnly);
 
-            // Modify input timestamp to force a re-build and re-link
+            // Remove root descriptor to change the linker behavior.
             WaitForUtcNowToAdvance();
-            File.SetLastWriteTimeUtc(Path.Combine(testAsset.TestRoot, testProject.Name, $"{projectName}.cs"), DateTime.UtcNow);
+            // File.SetLastWriteTimeUtc(Path.Combine(testAsset.TestRoot, testProject.Name, $"{projectName}.cs"), DateTime.UtcNow);
+            testAsset = testAsset.WithProjectChanges(project => RemoveRootDescriptor(project));
 
             // Link, discarding classlib
             publishCommand.Execute($"/p:RuntimeIdentifier={rid}", $"/p:SelfContained=true", "/p:PublishTrimmed=true").Should().Pass();
+            DateTime semaphoreSecondModifiedTime = File.GetLastWriteTimeUtc(linkSemaphore);
+
+            // Check that the linker actually ran again
+            semaphoreFirstModifiedTime.Should().NotBe(semaphoreSecondModifiedTime);
+
             File.Exists(linkedDllKeptFirstTimeOnly).Should().BeFalse();
             File.Exists(publishedDllKeptFirstTimeOnly).Should().BeFalse();
 
@@ -270,6 +287,25 @@ private TestPackageReference GetPackageReference(TestProject project)
             return new TestPackageReference(project.Name, "1.0.0", pack.GetNuGetPackage(project.Name));
         }
 
+        private void AddRootDescriptor(XDocument project, string rootDescriptorFileName)
+        {
+            var ns = project.Root.Name.Namespace;
+
+            var itemGroup = new XElement(ns + "ItemGroup");
+            project.Root.Add(itemGroup);
+            itemGroup.Add(new XElement(ns + "TrimmerRootDescriptor",
+                                       new XAttribute("Include", rootDescriptorFileName)));
+        }
+
+        private void RemoveRootDescriptor(XDocument project)
+        {
+            var ns = project.Root.Name.Namespace;
+
+            project.Root.Elements(ns + "ItemGroup")
+                .Where(ig => ig.Elements(ns + "TrimmerRootDescriptor").Any())
+                .First().Remove();
+        }
+
         private TestProject CreateTestProjectForILLinkTesting(string targetFramework, string mainProjectName, string referenceProjectName)
         {
             var referenceProject = new TestProject()