The present invention provides a method for upgrading embedded configuration databases while a network device is operating and with minimal disruption to network device operation. While a network device is operating and using an embedded primary configuration database, an embedded backup configuration database stops performing as a backup database and is upgraded. The upgraded configuration database is then switched over to become the primary configuration database. The original primary configuration database may immediately become the backup configuration database, or the original primary configuration database may remain unchanged until the upgrade is committed. If the upgrade is not committed, for example, due to errors, then the original primary configuration database may be quickly switched over to again become the primary configuration database. As a result, embedded configuration databases may be upgraded while a network device is operating and with minimal disruption to network device operation.