diff --git a/docs/changelog.md b/docs/changelog.md
index 705e529f5..9503c48f6 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -14,6 +14,9 @@ Requires libvips v8.15.1
   [#4028](https://github.com/lovell/sharp/pull/4028)
   [@yolopunk](https://github.com/yolopunk)
 
+* Ensure `clone` takes a deep copy of existing options.
+  [#4029](https://github.com/lovell/sharp/issues/4029)
+
 ### v0.33.2 - 12th January 2024
 
 * Upgrade to libvips v8.15.1 for upstream bug fixes.
diff --git a/lib/constructor.js b/lib/constructor.js
index dd2c4e394..05b4c2db3 100644
--- a/lib/constructor.js
+++ b/lib/constructor.js
@@ -425,13 +425,16 @@ Object.setPrototypeOf(Sharp, stream.Duplex);
 function clone () {
   // Clone existing options
   const clone = this.constructor.call();
-  clone.options = Object.assign({}, this.options);
+  const { debuglog, queueListener, ...options } = this.options;
+  clone.options = structuredClone(options);
+  clone.options.debuglog = debuglog;
+  clone.options.queueListener = queueListener;
   // Pass 'finish' event to clone for Stream-based input
   if (this._isStreamInput()) {
     this.on('finish', () => {
       // Clone inherits input data
       this._flattenBufferIn();
-      clone.options.bufferIn = this.options.bufferIn;
+      clone.options.input.buffer = this.options.input.buffer;
       clone.emit('finish');
     });
   }
diff --git a/test/unit/clone.js b/test/unit/clone.js
index 690792db9..0db81ae53 100644
--- a/test/unit/clone.js
+++ b/test/unit/clone.js
@@ -77,4 +77,26 @@ describe('Clone', function () {
     assert.strictEqual(0, original.listenerCount('finish'));
     assert.strictEqual(0, clone.listenerCount('finish'));
   });
+
+  it('Ensure deep clone of properties, including arrays', async () => {
+    const alpha = await sharp({
+      create: { width: 320, height: 240, channels: 3, background: 'red' }
+    }).toColourspace('b-w').png().toBuffer();
+
+    const original = sharp();
+    const joiner = original.clone().joinChannel(alpha);
+    const negater = original.clone().negate();
+
+    fs.createReadStream(fixtures.inputJpg320x240).pipe(original);
+    const joined = await joiner.png({ effort: 1 }).toBuffer();
+    const negated = await negater.png({ effort: 1 }).toBuffer();
+
+    const joinedMetadata = await sharp(joined).metadata();
+    assert.strictEqual(joinedMetadata.channels, 4);
+    assert.strictEqual(joinedMetadata.hasAlpha, true);
+
+    const negatedMetadata = await sharp(negated).metadata();
+    assert.strictEqual(negatedMetadata.channels, 3);
+    assert.strictEqual(negatedMetadata.hasAlpha, false);
+  });
 });