A programmatic method for automatically backing up and restoring an integrated database system including a Lotus Notes/Domino loosely structured database and a linked DB2 relational database that stores data mapped from the Domino database. The method includes integrated first and second client application programs running on server hosts for backup and recovery of the Domino and DB2 databases that communicate with the database managers for the databases using client application APIs. Backup and recovery of the integrated linked databases is controlled by the client application associated with the Domino database.