St. Peter's derives its "surname" Merton from Merton Priory, in Surrey, which owned the church. The church was founded in 1117 by Gilbert the Norman, one time sheriff of Surrey, Cambridge and Huntingdon, and godson of Henry I.
The original building was late Saxon. Remains of that early building are still to be found; parts of the chancel were contained in the original nave of the Saxon church. Quoins in the chancel and beside the west arch are also pre-Conquest.
The Norman south door is an impressive import from another Bedford church, St. Peter de Dunstable, which was torn down in 1545.
