diff --git a/src/plugins/projectexplorer/appoutputpane.cpp b/src/plugins/projectexplorer/appoutputpane.cpp
index bde29975791..e0969dc8df7 100644
--- a/src/plugins/projectexplorer/appoutputpane.cpp
+++ b/src/plugins/projectexplorer/appoutputpane.cpp
@@ -101,7 +101,7 @@ void TabWidget::slotContextMenuRequested(const QPoint &pos)
 }
 
 AppOutputPane::RunControlTab::RunControlTab(RunControl *rc, Core::OutputWindow *w) :
-    runControl(rc), window(w), asyncClosing(false)
+    runControl(rc), window(w), asyncClosing(false), behavivorOnOutput(Flash)
 {
 }
 
@@ -360,8 +360,16 @@ void AppOutputPane::updateFromSettings()
 void AppOutputPane::appendMessage(RunControl *rc, const QString &out, Utils::OutputFormat format)
 {
     const int index = indexOf(rc);
-    if (index != -1)
-        m_runControlTabs.at(index).window->appendMessage(out, format);
+    if (index != -1) {
+        Core::OutputWindow *window = m_runControlTabs.at(index).window;
+        window->appendMessage(out, format);
+        if (format != Utils::NormalMessageFormat) {
+            if (m_runControlTabs.at(index).behavivorOnOutput == Flash)
+                flash();
+            else
+                popup(NoModeSwitch);
+        }
+    }
 }
 
 void AppOutputPane::showTabFor(RunControl *rc)
@@ -369,6 +377,13 @@ void AppOutputPane::showTabFor(RunControl *rc)
     m_tabWidget->setCurrentIndex(tabWidgetIndexOf(indexOf(rc)));
 }
 
+void AppOutputPane::setBehaviorOnOutput(RunControl *rc, AppOutputPane::BehavivorOnOutput mode)
+{
+    const int index = indexOf(rc);
+    if (index != -1)
+        m_runControlTabs[index].behavivorOnOutput = mode;
+}
+
 void AppOutputPane::reRunRunControl()
 {
     const int index = currentIndex();
diff --git a/src/plugins/projectexplorer/appoutputpane.h b/src/plugins/projectexplorer/appoutputpane.h
index 1263a89585a..af9dc3fa0bb 100644
--- a/src/plugins/projectexplorer/appoutputpane.h
+++ b/src/plugins/projectexplorer/appoutputpane.h
@@ -60,6 +60,11 @@ public:
         CloseTabWithPrompt
     };
 
+    enum BehavivorOnOutput {
+        Flash,
+        Popup
+    };
+
     AppOutputPane();
     virtual ~AppOutputPane();
 
@@ -81,6 +86,7 @@ public:
 
     void createNewOutputWindow(RunControl *rc);
     void showTabFor(RunControl *rc);
+    void setBehaviorOnOutput(RunControl *rc, BehavivorOnOutput mode);
 
     bool aboutToClose() const;
     bool closeTabs(CloseTabMode mode);
@@ -124,6 +130,7 @@ private:
         Core::OutputWindow *window;
         // Is the run control stopping asynchronously, close the tab once it finishes
         bool asyncClosing;
+        BehavivorOnOutput behavivorOnOutput;
     };
 
     bool isRunning() const;
diff --git a/src/plugins/projectexplorer/projectexplorer.cpp b/src/plugins/projectexplorer/projectexplorer.cpp
index 16d9b6d8289..b1cd8b0a29a 100644
--- a/src/plugins/projectexplorer/projectexplorer.cpp
+++ b/src/plugins/projectexplorer/projectexplorer.cpp
@@ -1685,12 +1685,12 @@ void ProjectExplorerPlugin::showRunErrorMessage(const QString &errorMessage)
 void ProjectExplorerPlugin::startRunControl(RunControl *runControl, RunMode runMode)
 {
     d->m_outputPane->createNewOutputWindow(runControl);
-    if (runMode == NormalRunMode && d->m_projectExplorerSettings.showRunOutput)
-        d->m_outputPane->popup(Core::IOutputPane::NoModeSwitch);
-    if ((runMode == DebugRunMode || runMode == DebugRunModeWithBreakOnMain)
-            && d->m_projectExplorerSettings.showDebugOutput)
-        d->m_outputPane->popup(Core::IOutputPane::NoModeSwitch);
+    d->m_outputPane->flash(); // one flash for starting
     d->m_outputPane->showTabFor(runControl);
+    bool popup = (runMode == NormalRunMode && d->m_projectExplorerSettings.showRunOutput)
+            || ((runMode == DebugRunMode || runMode == DebugRunModeWithBreakOnMain)
+                && d->m_projectExplorerSettings.showDebugOutput);
+    d->m_outputPane->setBehaviorOnOutput(runControl, popup ? AppOutputPane::Popup : AppOutputPane::Flash);
     connect(runControl, SIGNAL(finished()), this, SLOT(runControlFinished()));
     runControl->start();
     emit updateRunActions();
diff --git a/src/plugins/projectexplorer/projectexplorersettingspage.ui b/src/plugins/projectexplorer/projectexplorersettingspage.ui
index c1b27df012b..9bfc39b131f 100644
--- a/src/plugins/projectexplorer/projectexplorersettingspage.ui
+++ b/src/plugins/projectexplorer/projectexplorersettingspage.ui
@@ -113,7 +113,16 @@
       <item row="3" column="1">
        <widget class="QWidget" name="widget" native="true">
         <layout class="QHBoxLayout" name="horizontalLayout">
-         <property name="margin">
+         <property name="leftMargin">
+          <number>0</number>
+         </property>
+         <property name="topMargin">
+          <number>0</number>
+         </property>
+         <property name="rightMargin">
+          <number>0</number>
+         </property>
+         <property name="bottomMargin">
           <number>0</number>
          </property>
          <item>
@@ -152,14 +161,14 @@
       <item row="4" column="0">
        <widget class="QCheckBox" name="showRunOutputCheckBox">
         <property name="text">
-         <string>Open application output pane when running</string>
+         <string>Open application output pane on output when running</string>
         </property>
        </widget>
       </item>
       <item row="5" column="0">
        <widget class="QCheckBox" name="showDebugOutputCheckBox">
         <property name="text">
-         <string>Open application output pane when debugging</string>
+         <string>Open application output pane on output when debugging</string>
         </property>
        </widget>
       </item>