diff --git a/src/document/document.ts b/src/document/document.ts
index 601b24655..d5b5f8f29 100644
--- a/src/document/document.ts
+++ b/src/document/document.ts
@@ -977,6 +977,13 @@ export class Document<T, P extends Indexable = Indexable> {
     return this.root.getGarbageLen();
   }
 
+  /**
+   * `getGarbageLenFromClone` returns the length of elements should be purged from clone.
+   */
+  public getGarbageLenFromClone(): number {
+    return this.clone!.root.getGarbageLen();
+  }
+
   /**
    * `toJSON` returns the JSON encoding of this document.
    */
diff --git a/src/document/operation/set_operation.ts b/src/document/operation/set_operation.ts
index dae98d860..88884ff44 100644
--- a/src/document/operation/set_operation.ts
+++ b/src/document/operation/set_operation.ts
@@ -68,8 +68,12 @@ export class SetOperation extends Operation {
     }
     const obj = parentObject as CRDTObject;
     const value = this.value.deepcopy();
-    obj.set(this.key, value);
+    const removed = obj.set(this.key, value);
     root.registerElement(value, obj);
+    if (removed) {
+      root.registerRemovedElement(removed);
+    }
+
     return {
       opInfos: [
         {
diff --git a/test/integration/gc_test.ts b/test/integration/gc_test.ts
index 9a8142646..3ea460201 100644
--- a/test/integration/gc_test.ts
+++ b/test/integration/gc_test.ts
@@ -586,4 +586,27 @@ describe('Garbage Collection', function () {
     await client1.deactivate();
     await client2.deactivate();
   });
+
+  it('Can collect removed elements from both root and clone', async function ({
+    task,
+  }) {
+    type TestDoc = { point: { x: number; y: number } };
+    const docKey = toDocKey(`${task.name}-${new Date().getTime()}`);
+    const doc = new yorkie.Document<TestDoc>(docKey);
+    const cli = new yorkie.Client(testRPCAddr);
+    await cli.activate();
+
+    await cli.attach(doc, { isRealtimeSync: false });
+    doc.update((root) => {
+      root.point = { x: 0, y: 0 };
+    });
+    doc.update((root) => {
+      root.point = { x: 1, y: 1 };
+    });
+    doc.update((root) => {
+      root.point = { x: 2, y: 2 };
+    });
+    assert.equal(doc.getGarbageLen(), 6);
+    assert.equal(doc.getGarbageLenFromClone(), 6);
+  });
 });
diff --git a/test/unit/document/document_test.ts b/test/unit/document/document_test.ts
index ea326bd6b..ccdac7e8f 100644
--- a/test/unit/document/document_test.ts
+++ b/test/unit/document/document_test.ts
@@ -1189,7 +1189,7 @@ describe.sequential('Document', function () {
       delete root.a;
     });
     assert.equal('{}', doc.toSortedJSON());
-    assert.equal(1, doc.getGarbageLen());
+    assert.equal(2, doc.getGarbageLen());
 
     doc.garbageCollect(MaxTimeTicket);
     assert.equal('{}', doc.toSortedJSON());