diff --git a/mojo/android/javatests/mojo_test_case.cc b/mojo/android/javatests/mojo_test_case.cc
index f958d7c0d72b58..22a08ff674fcd2 100644
--- a/mojo/android/javatests/mojo_test_case.cc
+++ b/mojo/android/javatests/mojo_test_case.cc
@@ -54,8 +54,7 @@ static void RunLoop(JNIEnv* env,
   base::RunLoop run_loop;
   if (timeout_ms) {
     base::MessageLoop::current()->PostDelayedTask(
-        FROM_HERE,
-        base::MessageLoop::QuitClosure(),
+        FROM_HERE, base::MessageLoop::QuitWhenIdleClosure(),
         base::TimeDelta::FromMilliseconds(timeout_ms));
     run_loop.Run();
   } else {
diff --git a/mojo/android/system/base_run_loop.cc b/mojo/android/system/base_run_loop.cc
index df78561b27de3d..e48d2f0e019947 100644
--- a/mojo/android/system/base_run_loop.cc
+++ b/mojo/android/system/base_run_loop.cc
@@ -39,7 +39,7 @@ static void RunUntilIdle(JNIEnv* env,
 static void Quit(JNIEnv* env,
                  const JavaParamRef<jobject>& jcaller,
                  jlong runLoopID) {
-  reinterpret_cast<base::MessageLoop*>(runLoopID)->Quit();
+  reinterpret_cast<base::MessageLoop*>(runLoopID)->QuitWhenIdle();
 }
 
 static void RunJavaRunnable(
diff --git a/mojo/application/public/cpp/lib/application_impl.cc b/mojo/application/public/cpp/lib/application_impl.cc
index 7ea8834bd17ee5..aecd61cdd5b56b 100644
--- a/mojo/application/public/cpp/lib/application_impl.cc
+++ b/mojo/application/public/cpp/lib/application_impl.cc
@@ -20,7 +20,7 @@ namespace {
 void DefaultTerminationClosure() {
   if (base::MessageLoop::current() &&
       base::MessageLoop::current()->is_running())
-    base::MessageLoop::current()->Quit();
+    base::MessageLoop::current()->QuitWhenIdle();
 }
 
 }  // namespace
diff --git a/mojo/runner/android/background_application_loader_unittest.cc b/mojo/runner/android/background_application_loader_unittest.cc
index ac24ae5054309b..f99e44c3c31e95 100644
--- a/mojo/runner/android/background_application_loader_unittest.cc
+++ b/mojo/runner/android/background_application_loader_unittest.cc
@@ -20,7 +20,7 @@ class DummyLoader : public shell::ApplicationLoader {
   void Load(const GURL& url,
             InterfaceRequest<Application> application_request) override {
     if (simulate_app_quit_)
-      base::MessageLoop::current()->Quit();
+      base::MessageLoop::current()->QuitWhenIdle();
   }
 
   void DontSimulateAppQuit() { simulate_app_quit_ = false; }
diff --git a/mojo/runner/context.cc b/mojo/runner/context.cc
index f1bb1a468ae26b..462ed84d350d84 100644
--- a/mojo/runner/context.cc
+++ b/mojo/runner/context.cc
@@ -259,7 +259,7 @@ void Context::Shutdown() {
 void Context::OnShutdownComplete() {
   DCHECK_EQ(base::MessageLoop::current()->task_runner(),
             task_runners_->shell_runner());
-  base::MessageLoop::current()->Quit();
+  base::MessageLoop::current()->QuitWhenIdle();
 }
 
 void Context::Run(const GURL& url) {
@@ -302,7 +302,7 @@ void Context::OnApplicationEnd(const GURL& url) {
       DCHECK_EQ(base::MessageLoop::current()->task_runner(),
                 task_runners_->shell_runner());
       if (app_complete_callback_.is_null()) {
-        base::MessageLoop::current()->Quit();
+        base::MessageLoop::current()->QuitWhenIdle();
       } else {
         app_complete_callback_.Run();
       }
diff --git a/mojo/runner/native_runner_unittest.cc b/mojo/runner/native_runner_unittest.cc
index d75373841c8fdb..b2516b0547942d 100644
--- a/mojo/runner/native_runner_unittest.cc
+++ b/mojo/runner/native_runner_unittest.cc
@@ -33,7 +33,7 @@ class TestNativeRunner : public shell::NativeRunner {
   ~TestNativeRunner() override {
     state_->runner_was_destroyed = true;
     if (base::MessageLoop::current()->is_running())
-      base::MessageLoop::current()->Quit();
+      base::MessageLoop::current()->QuitWhenIdle();
   }
   void Start(const base::FilePath& app_path,
              bool start_sandboxed,
diff --git a/mojo/runner/shell_apptest.cc b/mojo/runner/shell_apptest.cc
index 13ddf36e7b8339..f0eb95cf1afdcf 100644
--- a/mojo/runner/shell_apptest.cc
+++ b/mojo/runner/shell_apptest.cc
@@ -124,7 +124,7 @@ TEST_F(ShellHTTPAppTest, Http) {
                    EXPECT_EQ(GetURL("app"), app_url);
                    EXPECT_EQ(GetURL("app"), connection_url);
                    EXPECT_EQ("hello", message);
-                   base::MessageLoop::current()->Quit();
+                   base::MessageLoop::current()->QuitWhenIdle();
                  });
   base::RunLoop().Run();
 }
@@ -140,7 +140,7 @@ TEST_F(ShellHTTPAppTest, Redirect) {
                    EXPECT_EQ(GetURL("app"), app_url);
                    EXPECT_EQ(GetURL("app"), connection_url);
                    EXPECT_EQ("hello", message);
-                   base::MessageLoop::current()->Quit();
+                   base::MessageLoop::current()->QuitWhenIdle();
                  });
   base::RunLoop().Run();
 }
@@ -169,7 +169,7 @@ TEST_F(ShellHTTPAppTest, MAYBE_QueryHandling) {
       EXPECT_EQ(GetURL("app?foo"), connection_url);
     } else if (num_responses == 2) {
       EXPECT_EQ(GetURL("app?bar"), connection_url);
-      base::MessageLoop::current()->Quit();
+      base::MessageLoop::current()->QuitWhenIdle();
     } else {
       CHECK(false);
     }
@@ -189,7 +189,7 @@ TEST_F(ShellAppTest, MojoURLQueryHandling) {
                                base::CompareCase::SENSITIVE));
     EXPECT_EQ(app_url.To<std::string>() + "?foo", connection_url);
     EXPECT_EQ("hello", message);
-    base::MessageLoop::current()->Quit();
+    base::MessageLoop::current()->QuitWhenIdle();
   };
   pingable->Ping("hello", callback);
   base::RunLoop().Run();
diff --git a/mojo/services/test_service/test_service_application.cc b/mojo/services/test_service/test_service_application.cc
index 2c1569c89cb3c6..7fd16fadbe5b59 100644
--- a/mojo/services/test_service/test_service_application.cc
+++ b/mojo/services/test_service/test_service_application.cc
@@ -53,7 +53,7 @@ void TestServiceApplication::ReleaseRef() {
   assert(ref_count_ > 0);
   ref_count_--;
   if (ref_count_ <= 0)
-    base::MessageLoop::current()->Quit();
+    base::MessageLoop::current()->QuitWhenIdle();
 }
 
 }  // namespace test
diff --git a/mojo/shell/application_manager_unittest.cc b/mojo/shell/application_manager_unittest.cc
index 058240cee61817..e13f616f5573d6 100644
--- a/mojo/shell/application_manager_unittest.cc
+++ b/mojo/shell/application_manager_unittest.cc
@@ -54,7 +54,7 @@ class TestServiceImpl : public TestService {
     --context_->num_impls;
     if (!base::MessageLoop::current()->is_running())
       return;
-    base::MessageLoop::current()->Quit();
+    base::MessageLoop::current()->QuitWhenIdle();
   }
 
   // TestService implementation:
@@ -76,7 +76,7 @@ class TestClient {
 
   void AckTest() {
     if (quit_after_ack_)
-      base::MessageLoop::current()->Quit();
+      base::MessageLoop::current()->QuitWhenIdle();
   }
 
   void Test(const std::string& test_string) {
@@ -268,7 +268,7 @@ class TestAImpl : public TestA {
   }
 
   void Quit() {
-    base::MessageLoop::current()->Quit();
+    base::MessageLoop::current()->QuitWhenIdle();
     test_context_->set_a_called_quit();
     test_context_->QuitSoon();
   }
@@ -291,7 +291,7 @@ class TestBImpl : public TestB {
   ~TestBImpl() override {
     test_context_->IncrementNumBDeletes();
     if (base::MessageLoop::current()->is_running())
-      base::MessageLoop::current()->Quit();
+      base::MessageLoop::current()->QuitWhenIdle();
     test_context_->QuitSoon();
   }
 
@@ -351,7 +351,7 @@ class Tester : public ApplicationDelegate,
         requestor_url_ != connection->GetRemoteApplicationURL()) {
       context_->set_tester_called_quit();
       context_->QuitSoon();
-      base::MessageLoop::current()->Quit();
+      base::MessageLoop::current()->QuitWhenIdle();
       return false;
     }
     // If we're coming from A, then add B, otherwise A.
diff --git a/mojo/shell/capability_filter_test.cc b/mojo/shell/capability_filter_test.cc
index f8d0349e64608b..b50f7174dd817f 100644
--- a/mojo/shell/capability_filter_test.cc
+++ b/mojo/shell/capability_filter_test.cc
@@ -83,12 +83,12 @@ class ConnectionValidator : public ApplicationLoader,
     if (i != expectations_.end()) {
       expectations_.erase(i);
       if (expectations_.empty())
-        loop_->Quit();
+        loop_->QuitWhenIdle();
     } else {
       // This is a test failure, and will result in PrintUnexpectedExpecations()
       // being called.
       unexpected_.insert(result);
-      loop_->Quit();
+      loop_->QuitWhenIdle();
     }
   }