diff --git a/atom/browser/ui/win/notify_icon.cc b/atom/browser/ui/win/notify_icon.cc
index bc9ff46f939a..6cf207d7b8e1 100644
--- a/atom/browser/ui/win/notify_icon.cc
+++ b/atom/browser/ui/win/notify_icon.cc
@@ -4,7 +4,10 @@
 
 #include "atom/browser/ui/win/notify_icon.h"
 
+#include <shobjidl.h>
+
 #include "atom/browser/ui/win/notify_icon_host.h"
+#include "base/md5.h"
 #include "base/strings/string_number_conversions.h"
 #include "base/strings/utf_string_conversions.h"
 #include "base/win/windows_version.h"
@@ -26,9 +29,25 @@ NotifyIcon::NotifyIcon(NotifyIconHost* host,
       window_(window),
       message_id_(message),
       menu_model_(NULL) {
+
+  // NB: If we have an App Model ID, we should propagate that to the tray.
+  // Doing this prevents duplicate items from showing up in the notification
+  // preferences (i.e. "Always Show / Show notifications only / etc")
+  PWSTR explicit_app_id;
+
+  if (SUCCEEDED(GetCurrentProcessExplicitAppUserModelID(&explicit_app_id))) {
+    // GUIDs and MD5 hashes are the same length. So convenient!
+    base::MD5Sum(explicit_app_id,
+      sizeof(wchar_t) * wcslen(explicit_app_id),
+      (base::MD5Digest*)&tray_app_id_hash_);
+    has_tray_app_id_hash_ = true;
+
+    CoTaskMemFree(explicit_app_id);
+  }
+
   NOTIFYICONDATA icon_data;
   InitIconData(&icon_data);
-  icon_data.uFlags = NIF_MESSAGE;
+  icon_data.uFlags |= NIF_MESSAGE;
   icon_data.uCallbackMessage = message_id_;
   BOOL result = Shell_NotifyIcon(NIM_ADD, &icon_data);
   // This can happen if the explorer process isn't running when we try to
@@ -71,7 +90,7 @@ void NotifyIcon::ResetIcon() {
   // Delete any previously existing icon.
   Shell_NotifyIcon(NIM_DELETE, &icon_data);
   InitIconData(&icon_data);
-  icon_data.uFlags = NIF_MESSAGE;
+  icon_data.uFlags |= NIF_MESSAGE;
   icon_data.uCallbackMessage = message_id_;
   icon_data.hIcon = icon_.Get();
   // If we have an image, then set the NIF_ICON flag, which tells
@@ -88,7 +107,7 @@ void NotifyIcon::SetImage(const gfx::Image& image) {
   // Create the icon.
   NOTIFYICONDATA icon_data;
   InitIconData(&icon_data);
-  icon_data.uFlags = NIF_ICON;
+  icon_data.uFlags |= NIF_ICON;
   icon_.Set(IconUtil::CreateHICONFromSkBitmap(image.AsBitmap()));
   icon_data.hIcon = icon_.Get();
   BOOL result = Shell_NotifyIcon(NIM_MODIFY, &icon_data);
@@ -105,7 +124,7 @@ void NotifyIcon::SetToolTip(const std::string& tool_tip) {
   // Create the icon.
   NOTIFYICONDATA icon_data;
   InitIconData(&icon_data);
-  icon_data.uFlags = NIF_TIP;
+  icon_data.uFlags |= NIF_TIP;
   wcscpy_s(icon_data.szTip, base::UTF8ToUTF16(tool_tip).c_str());
   BOOL result = Shell_NotifyIcon(NIM_MODIFY, &icon_data);
   if (!result)
@@ -117,7 +136,7 @@ void NotifyIcon::DisplayBalloon(const gfx::Image& icon,
                                 const base::string16& contents) {
   NOTIFYICONDATA icon_data;
   InitIconData(&icon_data);
-  icon_data.uFlags = NIF_INFO;
+  icon_data.uFlags |= NIF_INFO;
   icon_data.dwInfoFlags = NIIF_INFO;
   wcscpy_s(icon_data.szInfoTitle, title.c_str());
   wcscpy_s(icon_data.szInfo, contents.c_str());
@@ -161,6 +180,13 @@ void NotifyIcon::InitIconData(NOTIFYICONDATA* icon_data) {
   icon_data->cbSize = sizeof(NOTIFYICONDATA);
   icon_data->hWnd = window_;
   icon_data->uID = icon_id_;
+
+  if (has_tray_app_id_hash_) {
+    icon_data->uFlags |= NIF_GUID;
+    memcpy(reinterpret_cast<void*>(&icon_data->guidItem),
+      &tray_app_id_hash_,
+      sizeof(GUID));
+  }
 }
 
 }  // namespace atom
diff --git a/atom/browser/ui/win/notify_icon.h b/atom/browser/ui/win/notify_icon.h
index 8e00f1267920..25ba8c8dc439 100644
--- a/atom/browser/ui/win/notify_icon.h
+++ b/atom/browser/ui/win/notify_icon.h
@@ -76,6 +76,10 @@ class NotifyIcon : public TrayIcon {
   // The context menu.
   ui::SimpleMenuModel* menu_model_;
 
+  // A hash of the app model ID
+  GUID tray_app_id_hash_;
+  bool has_tray_app_id_hash_;
+
   DISALLOW_COPY_AND_ASSIGN(NotifyIcon);
 };