The site has been used for Christian worship for more than a millennium. Although the current church is not that old and ruins of the earliest churches—probably build of wood—are no longer present, it does still house architectural artifacts among the oldest in Bedford. At one time, appointments within the church were made by the Augustinian Canons who had founded Merton Priory in Surrey. Their connection persists in the name 'de Merton' even though the English Crown took over patronage of St Peter after the Dissolution of the Monasteries of the 16th century. The rubble and cement tower of the church was constructed in Saxon times, as was an arch and a doorway which are set in the belfry's east wall. Notable Norman work in the church building includes an exterior doorway arch in the south porch. The chancel's font, priest's door and windows were added in the 13th and 14th centuries. A reproduction of an original fenestella from this time was added in the south wall of the sanctuary in the 19th century. As well as the 19th century additions to St Peter's previously mentioned, the church was enlarged at this time, and restoration work was undertaken. Additions included the vestry, aisles and west porch, as well as an extension to the nave. Work to the building in the 20th century included the paintings on the east wall, the tower ceiling decoration, the construction of the chapter house and the Burma Starstained glass window. Following the closure of the neighbouring parish church of St. Cuthberts in 1974, St. Peter's was also dedicated to Cuthbert of Lindisfarne.
St Peter's Church is an Anglican Parish Church in the heart of Bedford. The church is part of the Bedford Council of Faiths, and has many links to other churches and community groups. The church has strong links in particular with Bedford School located near to the church. Church services are held every Sunday 10.15am and at 9.00am and 4.00pm on the first Sunday of the month. The church has morning prayer on a Monday, Tuesday and Wednesday morning. Holy Communion is celebrated on Thursday at 10.30am. A coffee shop is open at the church on the second Saturday of the month from 10.30am for an hour.