diff --git a/src/comm/MAVLinkProtocol.cc b/src/comm/MAVLinkProtocol.cc
index d6743ff71ba977f73a8adfadf67606389d60b513..3b583080c7f7c7f7e1f382d42dcd77ff7f36a159 100644
--- a/src/comm/MAVLinkProtocol.cc
+++ b/src/comm/MAVLinkProtocol.cc
@@ -694,7 +694,11 @@ void MAVLinkProtocol::_startLogging(void)
 void MAVLinkProtocol::_stopLogging(void)
 {
     if (_closeLogFile()) {
-        emit saveTempFlightDataLog(_tempLogFile.fileName());
+        if (qgcApp()->promptFlightDataSave()) {
+            emit saveTempFlightDataLog(_tempLogFile.fileName());
+        } else {
+            QFile::remove(_tempLogFile.fileName());
+        }
     }
 }
 
diff --git a/src/qgcunittest/MainWindowTest.cc b/src/qgcunittest/MainWindowTest.cc
index 0ddb90868df81e396f8204c8723dfc0fbe89606d..408e95d870e695ec0dd530dc2b53161b4536bdb5 100644
--- a/src/qgcunittest/MainWindowTest.cc
+++ b/src/qgcunittest/MainWindowTest.cc
@@ -28,6 +28,8 @@
 
 #include "MainWindowTest.h"
 #include "QGCToolBar.h"
+#include "MockLink.h"
+#include "QGCMessageBox.h"
 
 UT_REGISTER_TEST(MainWindowTest)
 
@@ -66,3 +68,28 @@ void MainWindowTest::_clickThrough_test(void)
     }
     
 }
+
+void MainWindowTest::_connectWindowClose_test(void)
+{
+    LinkManager* linkMgr = LinkManager::instance();
+    Q_CHECK_PTR(linkMgr);
+    
+    MockLink* link = new MockLink();
+    Q_CHECK_PTR(link);
+    // FIXME: LinkManager/MainWindow needs to be re-architected so that you don't have to addLink to MainWindow to get things to work
+    _mainWindow->addLink(link);
+    linkMgr->connectLink(link);
+    QTest::qWait(5000); // Give enough time for UI to settle and heartbeats to go through
+    
+    // On MainWindow close we should get a message box telling the user to disconnect first
+    setExpectedMessageBox(QGCMessageBox::Ok);
+    _mainWindow->close();
+    QTest::qWait(1000); // Need to allow signals to move between threads    
+    checkExpectedMessageBox();
+
+    // We are going to disconnect the link which is going to pop a save file dialog
+    setExpectedFileDialog(getSaveFileName, QStringList());
+    linkMgr->disconnectLink(link);
+    QTest::qWait(1000); // Need to allow signals to move between threads
+    checkExpectedFileDialog();
+}
diff --git a/src/qgcunittest/MainWindowTest.h b/src/qgcunittest/MainWindowTest.h
index 47c9c20d6abdc4f01c2bd070bb47d636be77c395..87eb8270eafde5d5b2e59799ca00af8b23b11dac 100644
--- a/src/qgcunittest/MainWindowTest.h
+++ b/src/qgcunittest/MainWindowTest.h
@@ -44,6 +44,7 @@ private slots:
     void cleanup(void);
     
     void _clickThrough_test(void);
+    void _connectWindowClose_test(void);
     
 private:
     MainWindow* _mainWindow;
diff --git a/src/qgcunittest/MavlinkLogTest.cc b/src/qgcunittest/MavlinkLogTest.cc
index d23fbc0b9dc7e0ad8f512a4d97e9dc854cf46fd2..18cab63132ed3eb3feb185f979edfa853ab8f0d8 100644
--- a/src/qgcunittest/MavlinkLogTest.cc
+++ b/src/qgcunittest/MavlinkLogTest.cc
@@ -170,32 +170,3 @@ void MavlinkLogTest::_connectLog_test(void)
     QTest::qWait(1000); // Need to allow signals to move between threads to shutdown MainWindow
 }
 
-void MavlinkLogTest::_connectLogWindowClose_test(void)
-{
-    MainWindow* mainWindow = MainWindow::_create(NULL, MainWindow::CUSTOM_MODE_PX4);
-    Q_CHECK_PTR(mainWindow);
-    
-    LinkManager* linkMgr = LinkManager::instance();
-    Q_CHECK_PTR(linkMgr);
-    
-    MockLink* link = new MockLink();
-    Q_CHECK_PTR(link);
-    // FIXME: LinkManager/MainWindow needs to be re-architected so that you don't have to addLink to MainWindow to get things to work
-    mainWindow->addLink(link);
-    linkMgr->connectLink(link);
-    QTest::qWait(5000); // Give enough time for UI to settle and heartbeats to go through
-    
-    // On Disconnect: We should get a getSaveFileName dialog.
-    QDir logSaveDir(QStandardPaths::writableLocation(QStandardPaths::DocumentsLocation));
-    QString logSaveFile(logSaveDir.filePath(_saveLogFilename));
-    setExpectedFileDialog(getSaveFileName, QStringList(logSaveFile));
-    
-    // MainWindow deletes itself on close
-    mainWindow->close();
-    QTest::qWait(1000); // Need to allow signals to move between threads
-    
-    checkExpectedFileDialog();
-    
-    // Make sure the file is there and delete it
-    QCOMPARE(logSaveDir.remove(_saveLogFilename), true);
-}
diff --git a/src/qgcunittest/MavlinkLogTest.h b/src/qgcunittest/MavlinkLogTest.h
index 21cde409faf864484e9c65989861196f73984e27..b2a53a416404765c9ffef1de6afced2d6f3accf4 100644
--- a/src/qgcunittest/MavlinkLogTest.h
+++ b/src/qgcunittest/MavlinkLogTest.h
@@ -46,7 +46,6 @@ private slots:
     void _bootLogDetectionSave_test(void);
     void _bootLogDetectionZeroLength_test(void);
     void _connectLog_test(void);
-    void _connectLogWindowClose_test(void);
     
 private:
     void _createTempLogFile(bool zeroLength);
diff --git a/src/ui/MainWindow.cc b/src/ui/MainWindow.cc
index 8ed2ee9712ab650fb8a972fa6a0a1bbcfe7f4d5b..d43ec0750043b71ced897500f4b541366c36c5aa 100644
--- a/src/ui/MainWindow.cc
+++ b/src/ui/MainWindow.cc
@@ -778,12 +778,32 @@ void MainWindow::showHILConfigurationWidget(UASInterface* uas)
 
 void MainWindow::closeEvent(QCloseEvent *event)
 {
+    // Disallow window close if there are active connections
+    
+    bool foundConnections = false;
+    foreach(LinkInterface* link, LinkManager::instance()->getLinks()) {
+        if (link->isConnected()) {
+            foundConnections = true;
+            break;
+        }
+    }
+    
+    if (foundConnections) {
+        QGCMessageBox::warning(tr("QGroundControl close"), tr("There are still active connections to vehicles. Please disconnect all connections before closing QGroundControl."));
+        event->ignore();
+        return;
+    }
+
+    // Should not be any active connections
+    foreach(LinkInterface* link, LinkManager::instance()->getLinks()) {
+        Q_UNUSED(link);
+        Q_ASSERT(!link->isConnected());
+    }
+
     storeViewState();
     storeSettings();
     mavlink->storeSettings();
     UASManager::instance()->storeSettings();
-    // FIXME: If connected links, should prompt before close
-    LinkManager::instance()->disconnectAll();
     event->accept();
 }
 
@@ -1734,14 +1754,12 @@ bool MainWindow::dockWidgetTitleBarsEnabled() const
 
 void MainWindow::_saveTempFlightDataLog(QString tempLogfile)
 {
-    if (qgcApp()->promptFlightDataSave()) {
-        QString saveFilename = QGCFileDialog::getSaveFileName(this,
-                                                            tr("Select file to save Flight Data Log"),
-                                                            qgcApp()->mavlinkLogFilesLocation(),
-                                                            tr("Flight Data Log (*.mavlink)"));
-        if (!saveFilename.isEmpty()) {
-            QFile::copy(tempLogfile, saveFilename);
-        }
+    QString saveFilename = QGCFileDialog::getSaveFileName(this,
+                                                        tr("Select file to save Flight Data Log"),
+                                                        qgcApp()->mavlinkLogFilesLocation(),
+                                                        tr("Flight Data Log (*.mavlink)"));
+    if (!saveFilename.isEmpty()) {
+        QFile::copy(tempLogfile, saveFilename);
     }
     QFile::remove(tempLogfile);
 }