There was possibly a Saxon church here while a Norman church, with a tower at the west end of the south aisle, was built within the width of the High Street. Little remains of the this church except some rubble walling in the north west corner of the present nave. The church is known to have been dedicated to St. Peter by 1223. The church was rebuilt c.1460 in limestone ashlar with a chancel, north vestry and north and south chapels, an aisled and crenellated nave, a south porch with a priest's chamber over it, and a south west tower. In March 1498 the future Cardinal Wolsey was ordained here. From the later 16th century the dedication to St. Peter and St. Paul was used.
The church escaped the great fire of 1653. There are many wall monuments from the 17th to 19th centuries. Until 1843 there was a dove cote under the gabled roof above the stone vault of the chancel; a very rare feature in a church. The church was restored, including the replacement of the nave and aisle roofs, and the chancel refitted by T.H. Wyatt in 1862-3. In 1924 the benifce was united with that of St. Mary to become the rectory of Marlborough. In 1952 the parishes were united with St. Mary's as the parish church while on 1st November 1974 the church of St. Peter and St. Paul was made redundant.
It was made over for the use of the town in 1978 and has been used as an information centre and is now used as an outlet for selling locally made craft items and as a venue for exhibitions and concerts. The St. Peter's Trust, formed on 14th December 1977 and registered as a charity on 14th Decenber 1978, maintains the building. The parish registers from 1611 are held in the Wiltshire and Swindon History Centre in Chippenham.