diff --git a/atom/browser/api/atom_api_protocol.cc b/atom/browser/api/atom_api_protocol.cc
index c762559ab62c..8d542b36f9d7 100644
--- a/atom/browser/api/atom_api_protocol.cc
+++ b/atom/browser/api/atom_api_protocol.cc
@@ -26,6 +26,18 @@ namespace atom {
 
 namespace api {
 
+namespace {
+
+// Clear protocol handlers in IO thread.
+void ClearJobFactoryInIO(
+    scoped_refptr<brightray::URLRequestContextGetter> request_context_getter) {
+  auto job_factory = static_cast<AtomURLRequestJobFactory*>(
+      request_context_getter->job_factory());
+  job_factory->Clear();
+}
+
+}  // namespace
+
 Protocol::Protocol(v8::Isolate* isolate, AtomBrowserContext* browser_context)
     : request_context_getter_(static_cast<brightray::URLRequestContextGetter*>(
           browser_context->GetRequestContext())),
@@ -33,6 +45,12 @@ Protocol::Protocol(v8::Isolate* isolate, AtomBrowserContext* browser_context)
   Init(isolate);
 }
 
+Protocol::~Protocol() {
+  content::BrowserThread::PostTask(
+      content::BrowserThread::IO, FROM_HERE,
+      base::Bind(ClearJobFactoryInIO, request_context_getter_));
+}
+
 void Protocol::RegisterServiceWorkerSchemes(
     const std::vector<std::string>& schemes) {
   atom::AtomBrowserClient::SetCustomServiceWorkerSchemes(schemes);
diff --git a/atom/browser/api/atom_api_protocol.h b/atom/browser/api/atom_api_protocol.h
index 379c43bfcd78..b5d47def68c4 100644
--- a/atom/browser/api/atom_api_protocol.h
+++ b/atom/browser/api/atom_api_protocol.h
@@ -43,6 +43,7 @@ class Protocol : public mate::TrackableObject<Protocol> {
 
  protected:
   Protocol(v8::Isolate* isolate, AtomBrowserContext* browser_context);
+  ~Protocol();
 
  private:
   // Possible errors.
diff --git a/atom/browser/atom_access_token_store.cc b/atom/browser/atom_access_token_store.cc
index 9f57148120c8..21ef8edaece9 100644
--- a/atom/browser/atom_access_token_store.cc
+++ b/atom/browser/atom_access_token_store.cc
@@ -25,7 +25,6 @@ const char* kGeolocationProviderURL =
 }  // namespace
 
 AtomAccessTokenStore::AtomAccessTokenStore() {
-  LOG(ERROR) << "AtomAccessTokenStore";
   content::GeolocationProvider::GetInstance()->UserDidOptIntoLocationServices();
 }
 
diff --git a/atom/browser/net/atom_url_request_job_factory.cc b/atom/browser/net/atom_url_request_job_factory.cc
index d78b7026e563..d0caf183e91b 100644
--- a/atom/browser/net/atom_url_request_job_factory.cc
+++ b/atom/browser/net/atom_url_request_job_factory.cc
@@ -20,7 +20,7 @@ typedef net::URLRequestJobFactory::ProtocolHandler ProtocolHandler;
 AtomURLRequestJobFactory::AtomURLRequestJobFactory() {}
 
 AtomURLRequestJobFactory::~AtomURLRequestJobFactory() {
-  STLDeleteValues(&protocol_handler_map_);
+  Clear();
 }
 
 bool AtomURLRequestJobFactory::SetProtocolHandler(
@@ -77,6 +77,10 @@ bool AtomURLRequestJobFactory::HasProtocolHandler(
   return ContainsKey(protocol_handler_map_, scheme);
 }
 
+void AtomURLRequestJobFactory::Clear() {
+  STLDeleteValues(&protocol_handler_map_);
+}
+
 net::URLRequestJob* AtomURLRequestJobFactory::MaybeCreateJobWithProtocolHandler(
     const std::string& scheme,
     net::URLRequest* request,
diff --git a/atom/browser/net/atom_url_request_job_factory.h b/atom/browser/net/atom_url_request_job_factory.h
index ea2710bb4cf3..5b439c2f9cd8 100644
--- a/atom/browser/net/atom_url_request_job_factory.h
+++ b/atom/browser/net/atom_url_request_job_factory.h
@@ -39,6 +39,9 @@ class AtomURLRequestJobFactory : public net::URLRequestJobFactory {
   // Whether the protocol handler is registered by the job factory.
   bool HasProtocolHandler(const std::string& scheme) const;
 
+  // Clear all protocol handlers.
+  void Clear();
+
   // URLRequestJobFactory implementation
   net::URLRequestJob* MaybeCreateJobWithProtocolHandler(
       const std::string& scheme,