diff --git a/src/env.cc b/src/env.cc
index 36a1c1119dc8bd..dfd1e6385f829f 100644
--- a/src/env.cc
+++ b/src/env.cc
@@ -543,6 +543,8 @@ void Environment::CleanupHandles() {
   Isolate::DisallowJavascriptExecutionScope disallow_js(isolate(),
       Isolate::DisallowJavascriptExecutionScope::THROW_ON_FAILURE);
 
+  RunAndClearNativeImmediates(true /* skip SetUnrefImmediate()s */);
+
   for (ReqWrapBase* request : req_wrap_queue_)
     request->Cancel();
 
@@ -658,7 +660,7 @@ void Environment::AtExit(void (*cb)(void* arg), void* arg) {
   at_exit_functions_.push_front(ExitCallback{cb, arg});
 }
 
-void Environment::RunAndClearNativeImmediates() {
+void Environment::RunAndClearNativeImmediates(bool only_refed) {
   TraceEventScope trace_scope(TRACING_CATEGORY_NODE1(environment),
                               "RunAndClearNativeImmediates", this);
   size_t ref_count = 0;
@@ -675,7 +677,9 @@ void Environment::RunAndClearNativeImmediates() {
       if (head->is_refed())
         ref_count++;
 
-      head->Call(this);
+      if (head->is_refed() || !only_refed)
+        head->Call(this);
+
       if (UNLIKELY(try_catch.HasCaught())) {
         if (!try_catch.HasTerminated() && can_call_into_js())
           errors::TriggerUncaughtException(isolate(), try_catch);
diff --git a/src/env.h b/src/env.h
index 027f5c0bacfba1..c0c8ac0db4882d 100644
--- a/src/env.h
+++ b/src/env.h
@@ -1417,7 +1417,7 @@ class Environment : public MemoryRetainer {
   std::unique_ptr<NativeImmediateCallback> native_immediate_callbacks_head_;
   NativeImmediateCallback* native_immediate_callbacks_tail_ = nullptr;
 
-  void RunAndClearNativeImmediates();
+  void RunAndClearNativeImmediates(bool only_refed = false);
   static void CheckImmediate(uv_check_t* handle);
 
   // Use an unordered_set, so that we have efficient insertion and removal.
diff --git a/test/cctest/test_environment.cc b/test/cctest/test_environment.cc
index cc9b8e4531f6ef..0db2963acc9ba3 100644
--- a/test/cctest/test_environment.cc
+++ b/test/cctest/test_environment.cc
@@ -185,3 +185,26 @@ static void at_exit_js(void* arg) {
   assert(obj->IsObject());
   called_at_exit_js = true;
 }
+
+TEST_F(EnvironmentTest, SetImmediateCleanup) {
+  int called = 0;
+  int called_unref = 0;
+
+  {
+    const v8::HandleScope handle_scope(isolate_);
+    const Argv argv;
+    Env env {handle_scope, argv};
+
+    (*env)->SetImmediate([&](node::Environment* env_arg) {
+      EXPECT_EQ(env_arg, *env);
+      called++;
+    });
+    (*env)->SetUnrefImmediate([&](node::Environment* env_arg) {
+      EXPECT_EQ(env_arg, *env);
+      called_unref++;
+    });
+  }
+
+  EXPECT_EQ(called, 1);
+  EXPECT_EQ(called_unref, 0);
+}