diff --git a/src/Assets/TestProjects/TargetManifests/PrunePackages.xml b/src/Assets/TestProjects/TargetManifests/PrunePackages.xml
new file mode 100644
index 000000000000..d2841578b96f
--- /dev/null
+++ b/src/Assets/TestProjects/TargetManifests/PrunePackages.xml
@@ -0,0 +1,36 @@
+<Project Sdk="Microsoft.NET.Sdk">
+  <ItemGroup>
+    <PackageReference Include="Newtonsoft.Json" Version="9.0.1" />
+    <PackageReference Include="FluentAssertions" Version="5.10.3" />
+  </ItemGroup>
+    
+  <Target Name="AddPackagesToPrune" AfterTargets="PrepforRestoreForComposeStore">
+    <ItemGroup>
+      <PackageToPrune Include="Microsoft.CSharp" />
+      <PackageToPrune Include="System.Collections" />
+      <PackageToPrune Include="System.Diagnostics.Debug" />
+      <PackageToPrune Include="System.Dynamic.Runtime" />
+      <PackageToPrune Include="System.Globalization" />
+      <PackageToPrune Include="System.IO" />
+      <PackageToPrune Include="System.Linq" />
+      <PackageToPrune Include="System.Linq.Expressions" />
+      <PackageToPrune Include="System.ObjectModel" />
+      <PackageToPrune Include="System.Reflection" />
+      <PackageToPrune Include="System.Reflection.Extensions" />
+      <PackageToPrune Include="System.Resources.ResourceManager" />
+      <PackageToPrune Include="System.Runtime" />
+      <PackageToPrune Include="System.Runtime.Extensions" />
+      <PackageToPrune Include="System.Runtime.Serialization.Primitives" />
+      <PackageToPrune Include="System.Text.Encoding" />
+      <PackageToPrune Include="System.Text.Encoding.Extensions" />
+      <PackageToPrune Include="System.Text.RegularExpressions" />
+      <PackageToPrune Include="System.Threading" />
+      <PackageToPrune Include="System.Threading.Tasks" />
+      <PackageToPrune Include="System.Xml.ReaderWriter" />
+      <PackageToPrune Include="System.Xml.XDocument" />
+    </ItemGroup>
+    <PropertyGroup>
+      <PackagesToPrune>$(PackagesToPrune);@(PackageToPrune)</PackagesToPrune>
+    </PropertyGroup>
+  </Target>
+</Project>
\ No newline at end of file
diff --git a/src/Tasks/Microsoft.NET.Build.Tasks/FilterResolvedFiles.cs b/src/Tasks/Microsoft.NET.Build.Tasks/FilterResolvedFiles.cs
index 47c19f336ee7..e386a40dd910 100644
--- a/src/Tasks/Microsoft.NET.Build.Tasks/FilterResolvedFiles.cs
+++ b/src/Tasks/Microsoft.NET.Build.Tasks/FilterResolvedFiles.cs
@@ -69,7 +69,7 @@ protected override void ExecuteCore()
                 var pkgName = packageItem.ItemSpec;
                 if (!string.IsNullOrEmpty(pkgName))
                 {
-                    packageClosure.UnionWith(projectContext.GetTransitiveList(pkgName));
+                    packageClosure.UnionWith(projectContext.GetTransitiveList(pkgName, ignoreIfNotFound: true));
                 }
             }
 
diff --git a/src/Tasks/Microsoft.NET.Build.Tasks/ProjectContext.cs b/src/Tasks/Microsoft.NET.Build.Tasks/ProjectContext.cs
index 93541ac5674e..7db21df9c4a3 100644
--- a/src/Tasks/Microsoft.NET.Build.Tasks/ProjectContext.cs
+++ b/src/Tasks/Microsoft.NET.Build.Tasks/ProjectContext.cs
@@ -2,6 +2,7 @@
 // Licensed under the MIT license. See LICENSE file in the project root for full license information.
 
 using Microsoft.Build.Framework;
+using Microsoft.DotNet.PlatformAbstractions;
 using NuGet.Packaging.Core;
 using NuGet.ProjectModel;
 using System;
@@ -145,9 +146,13 @@ public IEnumerable<LockFileTargetLibrary> GetRuntimeLibraries(IEnumerable<string
             return runtimeLibraries.Filter(allExclusionList).ToArray();
         }
 
-        internal IEnumerable<PackageIdentity> GetTransitiveList(string package)
+        internal IEnumerable<PackageIdentity> GetTransitiveList(string package, bool ignoreIfNotFound = false)
         {
             LockFileTargetLibrary platformLibrary = _lockFileTarget.GetLibrary(package);
+            if (platformLibrary == null && ignoreIfNotFound)
+            {
+                return Enumerable.Empty<PackageIdentity>();
+            }
             IEnumerable<LockFileTargetLibrary> runtimeLibraries = _lockFileTarget.Libraries;
             Dictionary<string, LockFileTargetLibrary> libraryLookup =
                 runtimeLibraries.ToDictionary(e => e.Name, StringComparer.OrdinalIgnoreCase);
diff --git a/src/Tests/Microsoft.NET.Publish.Tests/GivenThatWeWantToStoreAProjectWithDependencies.cs b/src/Tests/Microsoft.NET.Publish.Tests/GivenThatWeWantToStoreAProjectWithDependencies.cs
index 0b2137897fa7..e0577c39cda2 100644
--- a/src/Tests/Microsoft.NET.Publish.Tests/GivenThatWeWantToStoreAProjectWithDependencies.cs
+++ b/src/Tests/Microsoft.NET.Publish.Tests/GivenThatWeWantToStoreAProjectWithDependencies.cs
@@ -340,6 +340,41 @@ public void It_stores_when_targeting_netcoreapp3(bool isExe)
             });
         }
 
+        [CoreMSBuildOnlyFact]
+        public void DotnetStoreWithPrunedPackages()
+        {
+            const string TargetFramework = "netcoreapp3.1";
+
+            TestAsset targetManifestsAsset = _testAssetsManager
+                .CopyTestAsset("TargetManifests")
+                .WithSource();
+
+            var outputFolder = Path.Combine(targetManifestsAsset.TestRoot, "o");
+            var workingDir = Path.Combine(targetManifestsAsset.TestRoot, "w");
+
+            var composeStore = new ComposeStoreCommand(Log, targetManifestsAsset.TestRoot, "PrunePackages.xml")
+                .Execute(
+                    $"/p:TargetFramework={TargetFramework}",
+                    $"/p:RuntimeIdentifier={EnvironmentInfo.GetCompatibleRid(TargetFramework)}",
+                    $"/p:ComposeDir={outputFolder}",
+                    $"/p:ComposeWorkingDir={workingDir}",
+                    "/p:PreserveComposeWorkingDir=true",
+                    "/p:DoNotDecorateComposeDir=true",
+                    "/p:CreateProfilingSymbols=false"
+                );
+
+            composeStore.Should().Pass();
+
+            new DirectoryInfo(outputFolder).GetDirectories()
+                .Select(d => d.Name)
+                .Should().BeEquivalentTo(
+                    "fluentassertions",
+                    "newtonsoft.json",
+                    "system.configuration.configurationmanager",
+                    "system.security.cryptography.protecteddata");
+
+        }
+
         private static HashSet<PackageIdentity> ParseStoreArtifacts(string path)
         {
             return new HashSet<PackageIdentity>(