diff --git a/src/tools/illink/src/linker/Linker.Steps/MarkStep.cs b/src/tools/illink/src/linker/Linker.Steps/MarkStep.cs
index 280f1908f79f03..0e95901f271aca 100644
--- a/src/tools/illink/src/linker/Linker.Steps/MarkStep.cs
+++ b/src/tools/illink/src/linker/Linker.Steps/MarkStep.cs
@@ -477,7 +477,6 @@ bool ProcessMarkedPending ()
 
 			foreach (var type in Annotations.GetPendingPreserve ()) {
 				marked = true;
-				Debug.Assert (Annotations.IsProcessed (type));
 				ApplyPreserveInfo (type);
 			}
 
@@ -2785,7 +2784,7 @@ void ApplyPreserveInfo (TypeDefinition type)
 
 			if (Annotations.TryGetPreserve (type, out TypePreserve preserve)) {
 				if (!Annotations.SetAppliedPreserve (type, preserve))
-					throw new InternalErrorException ($"Type {type} already has applied {preserve}.");
+					return;
 
 				var di = new DependencyInfo (DependencyKind.TypePreserve, type);
 
diff --git a/src/tools/illink/src/linker/Linker/Annotations.cs b/src/tools/illink/src/linker/Linker/Annotations.cs
index 68c8c320749966..bfcfe56e7d71e7 100644
--- a/src/tools/illink/src/linker/Linker/Annotations.cs
+++ b/src/tools/illink/src/linker/Linker/Annotations.cs
@@ -34,7 +34,6 @@
 using System.Diagnostics;
 using System.Diagnostics.CodeAnalysis;
 using System.Linq;
-using System.Reflection.Metadata.Ecma335;
 using ILLink.Shared.TrimAnalysis;
 using Mono.Cecil;
 using Mono.Cecil.Cil;
@@ -303,25 +302,12 @@ public bool SetAppliedPreserve (TypeDefinition type, TypePreserve preserve)
 			return true;
 		}
 
-		public bool HasAppliedPreserve (TypeDefinition type, TypePreserve preserve)
-		{
-			if (!preserved_types.TryGetValue (type, out (TypePreserve preserve, bool applied) existing))
-				throw new InternalErrorException ($"Type {type} must have a TypePreserve before it can be applied.");
-
-			if (preserve != existing.preserve)
-				throw new InternalErrorException ($"Type {type} does not have {preserve}. The TypePreserve may have changed before the call to {nameof (HasAppliedPreserve)}.");
-
-			return existing.applied;
-		}
-
 		public void SetPreserve (TypeDefinition type, TypePreserve preserve)
 		{
 			Debug.Assert (preserve != TypePreserve.Nothing);
 			if (!preserved_types.TryGetValue (type, out (TypePreserve preserve, bool applied) existing)) {
 				preserved_types.Add (type, (preserve, false));
 				if (IsProcessed (type)) {
-					// Required to track preserve for marked types where the existing preserve
-					// was Nothing (since these aren't explicitly tracked.)
 					var addedPending = pending_preserve.Add (type);
 					Debug.Assert (addedPending);
 				}
diff --git a/src/tools/illink/test/Mono.Linker.Tests.Cases/CommandLine/CustomStepApplyPreserve.cs b/src/tools/illink/test/Mono.Linker.Tests.Cases/CommandLine/CustomStepApplyPreserve.cs
new file mode 100644
index 00000000000000..ae48755d7fedfd
--- /dev/null
+++ b/src/tools/illink/test/Mono.Linker.Tests.Cases/CommandLine/CustomStepApplyPreserve.cs
@@ -0,0 +1,35 @@
+using System;
+using Mono.Linker.Tests.Cases.Expectations.Assertions;
+using Mono.Linker.Tests.Cases.Expectations.Metadata;
+
+namespace Mono.Linker.Tests.Cases.CommandLine
+{
+	[SetupCompileBefore ("CustomApplyPreserveStep.dll", new[] { "Dependencies/CustomApplyPreserveStep.cs" }, new[] { "illink.dll", "Mono.Cecil.dll" }, addAsReference: false)]
+	[SetupLinkerArgument ("--custom-step", "-MarkStep:CustomStep.CustomApplyPreserveStep,CustomApplyPreserveStep.dll")]
+	[SetupLinkerArgument ("--verbose")]
+	public class CustomStepApplyPreserve
+	{
+		[Kept]
+		public class HasPreserveApplied
+		{
+			[Kept]
+			public int Field;
+
+			[Kept]
+			public HasPreserveApplied () { }
+
+			[Kept]
+			public void Method ()
+			{
+			}
+
+			public class Nested { }
+		}
+
+		[Kept]
+		public static void Main ()
+		{
+			Console.WriteLine (typeof (HasPreserveApplied).FullName);
+		}
+	}
+}
diff --git a/src/tools/illink/test/Mono.Linker.Tests.Cases/CommandLine/Dependencies/CustomApplyPreserveStep.cs b/src/tools/illink/test/Mono.Linker.Tests.Cases/CommandLine/Dependencies/CustomApplyPreserveStep.cs
new file mode 100644
index 00000000000000..1975f2c357179a
--- /dev/null
+++ b/src/tools/illink/test/Mono.Linker.Tests.Cases/CommandLine/Dependencies/CustomApplyPreserveStep.cs
@@ -0,0 +1,13 @@
+namespace CustomStep
+{
+    public class CustomApplyPreserveStep : Mono.Linker.Steps.IStep
+    {
+        public void Process(Mono.Linker.LinkContext context)
+        {
+            var myType = context.GetType("Mono.Linker.Tests.Cases.CommandLine.CustomStepApplyPreserve/HasPreserveApplied");
+            context.Annotations.SetPreserve(myType, Mono.Linker.TypePreserve.Methods);
+            // Make sure we can set preserve multiple times
+            context.Annotations.SetPreserve(myType, Mono.Linker.TypePreserve.All);
+        }
+    }
+}
diff --git a/src/tools/illink/test/Mono.Linker.Tests.Cases/Mono.Linker.Tests.Cases.csproj b/src/tools/illink/test/Mono.Linker.Tests.Cases/Mono.Linker.Tests.Cases.csproj
index 2b025d9861a116..f54ae5639f9b75 100644
--- a/src/tools/illink/test/Mono.Linker.Tests.Cases/Mono.Linker.Tests.Cases.csproj
+++ b/src/tools/illink/test/Mono.Linker.Tests.Cases/Mono.Linker.Tests.Cases.csproj
@@ -22,6 +22,7 @@
     <Compile Remove="TypeForwarding\Dependencies\TypeForwardersRewriteForwarders.cs" />
     <Compile Remove="CommandLine\Dependencies\CustomStepDummy.cs" />
     <Compile Remove="CommandLine\Dependencies\CustomStepUser.cs" />
+    <Compile Remove="CommandLine\Dependencies\CustomApplyPreserveStep.cs" />
     <Compile Remove="Logging\Dependencies\LogStep.cs" />
     <Compile Remove="Extensibility\Dependencies\*.cs" />
     <Compile Remove="DynamicDependencies\Dependencies\FacadeAssembly.cs" />