diff --git a/src/calibre/db/backend.py b/src/calibre/db/backend.py
index 9a13f4fd21..3a8bca7df1 100644
--- a/src/calibre/db/backend.py
+++ b/src/calibre/db/backend.py
@@ -515,6 +515,7 @@ class DB(object):
     # }}}
 
     def initialize_custom_columns(self):  # {{{
+        self.custom_columns_deleted = False
         with self.conn:
             # Delete previously marked custom columns
             for record in self.conn.get(
@@ -537,6 +538,7 @@ class DB(object):
                         DROP TABLE   IF EXISTS {lt};
                         '''.format(table=table, lt=lt)
                 )
+                self.custom_columns_deleted = True
             self.conn.execute('DELETE FROM custom_columns WHERE mark_for_delete=1')
 
         # Load metadata for custom columns
diff --git a/src/calibre/db/cache.py b/src/calibre/db/cache.py
index ce7b48193f..6caa277508 100644
--- a/src/calibre/db/cache.py
+++ b/src/calibre/db/cache.py
@@ -107,6 +107,9 @@ class Cache(object):
 
         self._search_api = Search(self, 'saved_searches', self.field_metadata.get_search_terms())
         self.initialize_dynamic()
+        if self.backend.custom_columns_deleted:
+            self.mark_as_dirty(self.all_book_ids())
+        self.backend.custom_columns_deleted = False
 
     @write_api
     def initialize_dynamic(self):
@@ -1547,7 +1550,6 @@ class Cache(object):
     @write_api
     def delete_custom_column(self, label=None, num=None):
         self.backend.delete_custom_column(label, num)
-        self._mark_as_dirty(self._all_book_ids())
 
     @write_api
     def create_custom_column(self, label, name, datatype, is_multiple, editable=True, display={}):