diff --git a/packages/protobuf-bench/README.md b/packages/protobuf-bench/README.md
index fdc782599..ed2acd763 100644
--- a/packages/protobuf-bench/README.md
+++ b/packages/protobuf-bench/README.md
@@ -10,5 +10,5 @@ server would usually do.
 
 | code generator      | bundle size             | minified               | compressed         |
 |---------------------|------------------------:|-----------------------:|-------------------:|
-| protobuf-es         | 97,510 b      | 41,660 b | 10,845 b |
+| protobuf-es         | 97,734 b      | 41,763 b | 10,857 b |
 | protobuf-javascript | 394,384 b  | 288,654 b | 45,122 b |
diff --git a/packages/protobuf-test/src/clone.test.ts b/packages/protobuf-test/src/clone.test.ts
index 90b3aa1af..72860935a 100644
--- a/packages/protobuf-test/src/clone.test.ts
+++ b/packages/protobuf-test/src/clone.test.ts
@@ -15,6 +15,8 @@
 import { describe, expect } from "@jest/globals";
 import { MessageFieldMessage as TS_MessageFieldMessage } from "./gen/ts/extra/msg-message_pb.js";
 import { MessageFieldMessage as JS_MessageFieldMessage } from "./gen/js/extra/msg-message_pb.js";
+import { Empty as TS_Empty } from "./gen/ts/google/protobuf/empty_pb.js";
+import { Empty as JS_Empty } from "./gen/js/google/protobuf/empty_pb.js";
 import {
   RepeatedScalarValuesMessage as TS_RepeatedScalarValuesMessage,
   ScalarValuesMessage as TS_ScalarValuesMessage,
@@ -26,7 +28,7 @@ import {
 import { WrappersMessage as TS_WrappersMessage } from "./gen/ts/extra/wkt-wrappers_pb.js";
 import { WrappersMessage as JS_WrappersMessage } from "./gen/js/extra/wkt-wrappers_pb.js";
 import { testMT } from "./helpers.js";
-import { BoolValue, protoInt64 } from "@bufbuild/protobuf";
+import { BoolValue, WireType, protoInt64 } from "@bufbuild/protobuf";
 
 /* eslint-disable @typescript-eslint/ban-ts-comment */
 
@@ -146,4 +148,23 @@ describe("clone", function () {
     a.doubleValueField = 0.1;
     expect(b.doubleValueField).not.toBe(a.doubleValueField);
   });
+  // We are using Empty wkt to test unknown fields.
+  testMT({ ts: TS_Empty, js: JS_Empty }, (messageType) => {
+    const a = new messageType();
+    const bin = messageType.runtime.bin;
+    const unknownFields = [
+      { no: 1, wireType: WireType.Bit32, data: new Uint8Array([1, 2, 3, 4]) },
+    ];
+    for (const unknowField of unknownFields) {
+      bin.onUnknownField(
+        a,
+        unknowField.no,
+        unknowField.wireType,
+        unknowField.data,
+      );
+    }
+    const b = a.clone();
+    expect(b).toStrictEqual(a);
+    expect(bin.listUnknownFields(b)).toStrictEqual(unknownFields);
+  });
 });
diff --git a/packages/protobuf/src/message.ts b/packages/protobuf/src/message.ts
index 39552d547..cc9d3a1f1 100644
--- a/packages/protobuf/src/message.ts
+++ b/packages/protobuf/src/message.ts
@@ -40,6 +40,7 @@ export interface AnyMessage extends Message<AnyMessage> {
 export class Message<T extends Message<T> = AnyMessage> {
   /**
    * Compare with a message of the same type.
+   * Note that this function disregards extensions and unknown fields.
    */
   equals(other: T | PlainMessage<T> | undefined | null): boolean {
     return this.getType().runtime.util.equals(
diff --git a/packages/protobuf/src/private/util-common.ts b/packages/protobuf/src/private/util-common.ts
index c2e1a5400..42f4e6340 100644
--- a/packages/protobuf/src/private/util-common.ts
+++ b/packages/protobuf/src/private/util-common.ts
@@ -230,6 +230,9 @@ export function makeUtilCommon(): Omit<Util, "newFieldList" | "initFields"> {
         }
         any[member.localName] = copy;
       }
+      for (const uf of type.runtime.bin.listUnknownFields(message)) {
+        type.runtime.bin.onUnknownField(any, uf.no, uf.wireType, uf.data);
+      }
       return target;
     },
   };