2000
21 March, Archbishop Gleeson dies.

30 November, Bishop Philip Wilson (previously consecrated Bishop of Wollongong on 10 July 1996) is appointed as Archbishop Coadjutor cum jure successions.

2001
3 December, Archbishop Faulkner retires as Archbishop of Adelaide.

3 December, Archbishop Wilson is installed as Archbishop of Adelaide.

2003
2 February, Archbishop Wilson launches the Cathedral Associate Music Program, the new Associate Choir of Saint Francis Xavier Cathedral and the new Cathedral Solo Artists' Program. Joshua Valstar is instated as the Cathedral's inaugural Associate Director of Music. The program is to run at the Sunday 6 pm masses.

2004
The pews are restored and restained.

Plans are underway to repair the sinking eastern wall of the cathedral and to rebuild the pipe organ which was dismantled in 1994 to make way for the bells.

1 December, Statue of St Francis Xavier, previously located at St Francis Xavier Seminary, is placed in the cathedral narthex.