diff --git a/src/libraries/System.Security.Cryptography/tests/X509Certificates/ChainTests.cs b/src/libraries/System.Security.Cryptography/tests/X509Certificates/ChainTests.cs
index de1d0b55bf2f62..34ce9021b14b51 100644
--- a/src/libraries/System.Security.Cryptography/tests/X509Certificates/ChainTests.cs
+++ b/src/libraries/System.Security.Cryptography/tests/X509Certificates/ChainTests.cs
@@ -344,6 +344,8 @@ public static void BuildChainCustomTrustStore(
                 chainTest.ChainPolicy.TrustMode = X509ChainTrustMode.CustomRootTrust;
                 chainTest.ChainPolicy.ExtraStore.Add(issuerCert);
 
+                X509ChainStatusFlags allowedFlags = X509ChainStatusFlags.NoError;
+
                 switch (testArguments)
                 {
                     case BuildChainCustomTrustStoreTestArguments.TrustedIntermediateUntrustedRoot:
@@ -361,6 +363,9 @@ public static void BuildChainCustomTrustStore(
                         chainHolder.DisposeChainElements();
                         chainTest.ChainPolicy.CustomTrustStore.Remove(rootCert);
                         chainTest.ChainPolicy.TrustMode = X509ChainTrustMode.System;
+                        chainTest.ChainPolicy.VerificationFlags = X509VerificationFlags.AllowUnknownCertificateAuthority;
+                        chainTest.ChainPolicy.ExtraStore.Add(rootCert);
+                        allowedFlags |= X509ChainStatusFlags.UntrustedRoot;
                         break;
                     default:
                         throw new InvalidDataException();
@@ -368,7 +373,11 @@ public static void BuildChainCustomTrustStore(
 
                 Assert.Equal(chainBuildsSuccessfully, chainTest.Build(endCert));
                 Assert.Equal(3, chainTest.ChainElements.Count);
-                Assert.Equal(chainFlags, chainTest.AllStatusFlags());
+
+                X509ChainStatusFlags actualFlags = chainTest.AllStatusFlags();
+                actualFlags &= ~allowedFlags;
+
+                Assert.Equal(chainFlags, actualFlags);
             }
         }