diff --git a/src/calibre/gui2/ui.py b/src/calibre/gui2/ui.py
index cc2975e7a7..4667431d96 100644
--- a/src/calibre/gui2/ui.py
+++ b/src/calibre/gui2/ui.py
@@ -579,6 +579,9 @@ class Main(MainWindow, MainWindowMixin, DeviceMixin, # {{{
         except KeyboardInterrupt:
             pass
         time.sleep(2)
+        if mb is not None:
+            mb.flush()
+        QApplication.processEvents()
         self.hide_windows()
         return True
 
diff --git a/src/calibre/library/caches.py b/src/calibre/library/caches.py
index 0c3904532e..e18f514239 100644
--- a/src/calibre/library/caches.py
+++ b/src/calibre/library/caches.py
@@ -40,12 +40,14 @@ class MetadataBackup(Thread): # {{{
         self.get_metadata_for_dump = FunctionDispatcher(db.get_metadata_for_dump)
         self.clear_dirtied = FunctionDispatcher(db.clear_dirtied)
         self.set_dirtied = FunctionDispatcher(db.dirtied)
+        self.in_limbo = None
 
     def stop(self):
         self.keep_running = False
 
     def run(self):
         while self.keep_running:
+            self.in_limbo = None
             try:
                 time.sleep(0.5) # Limit to two per second
                 id_ = self.db.dirtied_queue.get(True, 1.45)
@@ -72,6 +74,7 @@ class MetadataBackup(Thread): # {{{
 
             if mi is None:
                 continue
+            self.in_limbo = id_
 
             # Give the GUI thread a chance to do something. Python threads don't
             # have priorities, so this thread would naturally keep the processor
@@ -99,6 +102,14 @@ class MetadataBackup(Thread): # {{{
                             'again, giving up')
                     continue
 
+    def flush(self):
+        'Used during shutdown to ensure that a dirtied book is not missed'
+        if self.in_limbo is not None:
+            try:
+                self.set_dirtied([self.in_limbo])
+            except:
+                traceback.print_exc()
+
     def write(self, path, raw):
         with open(path, 'wb') as f:
             f.write(raw)