diff --git a/src/api/api.cc b/src/api/api.cc
index 646d640870..05d70ef5ad 100644
--- a/src/api/api.cc
+++ b/src/api/api.cc
@@ -328,6 +328,7 @@ class CallDepthScope {
   bool CheckKeptObjectsClearedAfterMicrotaskCheckpoint(
       i::MicrotaskQueue* microtask_queue) {
     bool did_perform_microtask_checkpoint =
+        isolate_->thread_local_top()->CallDepthIsZero() &&
         do_callback && microtask_queue &&
         microtask_queue->microtasks_policy() == MicrotasksPolicy::kAuto;
     return !did_perform_microtask_checkpoint ||
diff --git a/test/mjsunit/harmony/weakrefs/clearkeptobjects-on-quit.js b/test/mjsunit/harmony/weakrefs/clearkeptobjects-on-quit.js
new file mode 100644
index 0000000000..6007f9c360
--- /dev/null
+++ b/test/mjsunit/harmony/weakrefs/clearkeptobjects-on-quit.js
@@ -0,0 +1,13 @@
+// Copyright 2020 the V8 project authors. All rights reserved.
+// Use of this source code is governed by a BSD-style license that can be
+// found in the LICENSE file.
+
+// Flags: --harmony-weak-refs
+
+// A newly created WeakRef is kept alive until the end of the next microtask
+// checkpoint. V8 asserts that the kept objects list is cleared at the end of
+// microtask checkpoints when the microtask policy is auto. Test that d8, which
+// uses the auto policy, upholds the assert when manually quitting.
+let obj = {};
+let wr = new WeakRef(obj);
+testRunner.quit();