diff --git a/app/src/cc/arduino/contributions/ContributionsSelfCheck.java b/app/src/cc/arduino/contributions/ContributionsSelfCheck.java
index 08c50d8b4..ed9f638c8 100644
--- a/app/src/cc/arduino/contributions/ContributionsSelfCheck.java
+++ b/app/src/cc/arduino/contributions/ContributionsSelfCheck.java
@@ -36,10 +36,14 @@ import cc.arduino.contributions.packages.filters.UpdatablePlatformPredicate;
 import cc.arduino.view.NotificationPopup;
 import processing.app.Base;
 import processing.app.BaseNoGui;
+import processing.app.Editor;
 import processing.app.I18n;
 
 import javax.swing.*;
 import javax.swing.event.HyperlinkListener;
+
+import java.awt.event.WindowEvent;
+import java.awt.event.WindowFocusListener;
 import java.util.TimerTask;
 
 import static processing.app.I18n.tr;
@@ -95,8 +99,30 @@ public class ContributionsSelfCheck extends TimerTask {
     }
 
     SwingUtilities.invokeLater(() -> {
-      notificationPopup = new NotificationPopup(base.getActiveEditor(), hyperlinkListener, text);
-      notificationPopup.setVisible(true);
+      Editor ed = base.getActiveEditor();
+      notificationPopup = new NotificationPopup(ed, hyperlinkListener, text);
+      if (ed.isFocused()) {
+        notificationPopup.begin();
+        return;
+      }
+
+      // If the IDE is not focused wait until it is focused again to
+      // display the notification, this avoids the annoying side effect
+      // to "steal" the focus from another application.
+      WindowFocusListener wfl = new WindowFocusListener() {
+        @Override
+        public void windowLostFocus(WindowEvent evt) {
+        }
+
+        @Override
+        public void windowGainedFocus(WindowEvent evt) {
+          notificationPopup.begin();
+          for (Editor e : base.getEditors())
+            e.removeWindowFocusListener(this);
+        }
+      };
+      for (Editor e : base.getEditors())
+        e.addWindowFocusListener(wfl);
     });
   }
 
diff --git a/app/src/cc/arduino/view/NotificationPopup.java b/app/src/cc/arduino/view/NotificationPopup.java
index f5dfc717e..87a8e3650 100644
--- a/app/src/cc/arduino/view/NotificationPopup.java
+++ b/app/src/cc/arduino/view/NotificationPopup.java
@@ -42,6 +42,8 @@ import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
+import java.util.Timer;
+import java.util.TimerTask;
 
 import javax.swing.ImageIcon;
 import javax.swing.JButton;
@@ -52,16 +54,18 @@ import javax.swing.WindowConstants;
 import javax.swing.border.LineBorder;
 import javax.swing.event.HyperlinkListener;
 
+import cc.arduino.Constants;
 import processing.app.Theme;
 
 public class NotificationPopup extends JDialog {
 
+  private Timer autoCloseTimer = new Timer(false);
+
   public NotificationPopup(Frame parent, HyperlinkListener hyperlinkListener,
                            String message) {
     super(parent, false);
     setLayout(new FlowLayout());
     setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
-    setAlwaysOnTop(true);
     setUndecorated(true);
     setResizable(false);
 
@@ -131,6 +135,17 @@ public class NotificationPopup extends JDialog {
   }
 
   public void close() {
+    autoCloseTimer.cancel();
     dispatchEvent(new WindowEvent(this, WindowEvent.WINDOW_CLOSING));
   }
+
+  public void begin() {
+    autoCloseTimer.schedule(new TimerTask() {
+      @Override
+      public void run() {
+        close();
+      }
+    }, Constants.NOTIFICATION_POPUP_AUTOCLOSE_DELAY);
+    setVisible(true);
+  }
 }
diff --git a/arduino-core/src/cc/arduino/Constants.java b/arduino-core/src/cc/arduino/Constants.java
index 6cc47c83a..3c90abe7d 100644
--- a/arduino-core/src/cc/arduino/Constants.java
+++ b/arduino-core/src/cc/arduino/Constants.java
@@ -44,7 +44,7 @@ public class Constants {
   public static final String LIBRARY_DEVELOPMENT_FLAG_FILE = ".development";
 
   public static final long BOARDS_LIBS_UPDATABLE_CHECK_START_PERIOD = 60000;
-  public static final int NOTIFICATION_POPUP_AUTOCLOSE_DELAY = 10000;
+  public static final long NOTIFICATION_POPUP_AUTOCLOSE_DELAY = 10000;
 
   public static final String PROXY_TYPE_NONE = "none";
   public static final String PROXY_TYPE_AUTO = "auto";
diff --git a/build/shared/revisions.txt b/build/shared/revisions.txt
index 3a4dcd68d..71607d2d7 100644
--- a/build/shared/revisions.txt
+++ b/build/shared/revisions.txt
@@ -3,6 +3,7 @@ ARDUINO 1.6.9
 [ide]
 * Catch and report errors during parsing contributed index files
 * Fixed IDE version color on about dialog box. Thanks @ivanebernal
+* The "always-on-top update notification" popup is now less intrusive.
 
 [core]
 * sam: Allow 3rd party boards that depend on SAM core to use their own