diff --git a/src/calibre/db/backend.py b/src/calibre/db/backend.py
index 7d4d4fb04d..bcf02f9704 100644
--- a/src/calibre/db/backend.py
+++ b/src/calibre/db/backend.py
@@ -27,7 +27,8 @@ from calibre.utils.icu import sort_key
 from calibre.utils.config import to_json, from_json, prefs, tweaks
 from calibre.utils.date import utcfromtimestamp, parse_date
 from calibre.utils.filenames import (
-    is_case_sensitive, samefile, hardlink_file, ascii_filename, WindowsAtomicFolderMove, atomic_rename)
+    is_case_sensitive, samefile, hardlink_file, ascii_filename,
+    WindowsAtomicFolderMove, atomic_rename, remove_dir_if_empty)
 from calibre.utils.magick.draw import save_cover_data_to
 from calibre.utils.formatter_functions import load_user_template_functions
 from calibre.db.tables import (OneToOneTable, ManyToOneTable, ManyToManyTable,
@@ -1184,8 +1185,7 @@ class DB(object):
         Read all data from the db into the python in-memory tables
         '''
 
-        with self.conn:  # Use a single transaction, to ensure nothing modifies
-                         # the db while we are reading
+        with self.conn:  # Use a single transaction, to ensure nothing modifies the db while we are reading
             for table in self.tables.itervalues():
                 try:
                     table.read(self)
@@ -1538,11 +1538,7 @@ class DB(object):
         if permanent:
             for path in paths:
                 self.rmtree(path)
-                try:
-                    os.rmdir(os.path.dirname(path))
-                except OSError as e:
-                    if e.errno != errno.ENOTEMPTY:
-                        raise
+                remove_dir_if_empty(os.path.dirname(path), ignore_metadata_caches=True)
         else:
             delete_service().delete_books(paths, self.library_path)
 
@@ -1666,6 +1662,4 @@ class DB(object):
         self.execute('UPDATE books SET path=? WHERE id=?', (path.replace(os.sep, '/'), book_id))
         vals = [(book_id, fmt, size, name) for fmt, size, name in formats]
         self.executemany('INSERT INTO data (book,format,uncompressed_size,name) VALUES (?,?,?,?)', vals)
-   # }}}
-
-
+    # }}}
diff --git a/src/calibre/db/delete_service.py b/src/calibre/db/delete_service.py
index 6d3e41ebbb..beda2ae954 100644
--- a/src/calibre/db/delete_service.py
+++ b/src/calibre/db/delete_service.py
@@ -11,6 +11,7 @@ from threading import Thread
 from Queue import Queue
 
 from calibre.ptempfile import remove_dir
+from calibre.utils.filenames import remove_dir_if_empty
 from calibre.utils.recycle_bin import delete_tree, delete_file
 
 class DeleteService(Thread):
@@ -93,10 +94,10 @@ class DeleteService(Thread):
                     time.sleep(1)
                     shutil.move(path, dest)
                 if delete_empty_parent:
-                    self.remove_dir_if_empty(os.path.dirname(path))
+                    remove_dir_if_empty(os.path.dirname(path), ignore_metadata_caches=True)
                 requests.append(dest)
         if not requests:
-            self.remove_dir_if_empty(tdir)
+            remove_dir_if_empty(tdir)
         else:
             self.requests.put(tdir)
 
diff --git a/src/calibre/db/tests/add_remove.py b/src/calibre/db/tests/add_remove.py
index 0c5443cfed..6fc81bba47 100644
--- a/src/calibre/db/tests/add_remove.py
+++ b/src/calibre/db/tests/add_remove.py
@@ -231,6 +231,8 @@ class AddRemoveTest(BaseTest):
         fmtpath = cache.format_abspath(1, 'FMT1')
         bookpath = os.path.dirname(fmtpath)
         authorpath = os.path.dirname(bookpath)
+        os.mkdir(os.path.join(authorpath, '.DS_Store'))
+        open(os.path.join(authorpath, 'Thumbs.db'), 'wb').close()
         item_id = {v:k for k, v in cache.fields['#series'].table.id_map.iteritems()}['My Series Two']
         cache.remove_books((1,), permanent=True)
         for x in (fmtpath, bookpath, authorpath):
diff --git a/src/calibre/utils/filenames.py b/src/calibre/utils/filenames.py
index 4bf1cffee3..e9a589fe8a 100644
--- a/src/calibre/utils/filenames.py
+++ b/src/calibre/utils/filenames.py
@@ -459,3 +459,34 @@ def atomic_rename(oldpath, newpath):
                 time.sleep(1)
     else:
         os.rename(oldpath, newpath)
+
+def remove_dir_if_empty(path, ignore_metadata_caches=False):
+    ''' Remove a directory if it is empty or contains only the folder metadata
+    caches from different OSes. To delete the folder if it contains only
+    metadata caches, set ignore_metadata_caches to True.'''
+    try:
+        os.rmdir(path)
+    except OSError as e:
+        if e.errno == errno.ENOTEMPTY or len(os.listdir(path)) > 0:
+            # Some linux systems appear to raise an EPERM instead of an
+            # ENOTEMPTY, see https://bugs.launchpad.net/bugs/1240797
+            if ignore_metadata_caches:
+                try:
+                    found = False
+                    for x in os.listdir(path):
+                        if x.lower() in {'.ds_store', 'thumbs.db'}:
+                            found = True
+                            x = os.path.join(path, x)
+                            if os.path.isdir(x):
+                                import shutil
+                                shutil.rmtree(x)
+                            else:
+                                os.remove(x)
+                except Exception:  # We could get an error, if, for example, windows has locked Thumbs.db
+                    found = False
+                if found:
+                    remove_dir_if_empty(path)
+            return
+        raise
+
+