This church consists of a western tower, nave, apsidal chancel, south porch and vestry, the inside walls are of red brick with black brick horizontal bands.
The origin of the church of St Peter is likely to be between the 1170s and 1270s. The church was never appropriated and remained under the management of the priory until the dissolution of monasteries in 1538. The church was described as having a chancel, nave and bell cote with a single bell and in 1602 was described as having defects which would be speedily repaired.
The site of the church is recorded as being to the north west of the church of St Mary and sharing a burial ground. St Peter's suffered from a low benefice and parish income thus falling into disrepair and in 1678 the benefice was combined with St Mary's. An order to demolish the church of St Peter was issued.
The church of St Mary was built in the main in the 13th and 15th centuries. There is sufficient evidence to believe that the present day church has the same basic structure from the original building. No evidence has been found to show that the church has been rebuilt, merely renovated and adapted in 1858 when Revd Windsor Berry came to the parish. The major change was the raising of the roof. There are three bells in the tower which cannot be rung because the bell frame is in need of expensive repair.
The bells are by George Heathcote between 1525 and 1558, Humphrey Wilkinson 1713 and Daniel Heathcote 1741. In 1864 it is reported 'it is with great pleasure that we announce the reopening of the parish church of Waddingham after having undergone a thorough restoration. The church had been rebuilt some years previously by the present Rector the Revd WW Berry. A new south porch had been built and the tower put into complete repair. New roofs had been added to the naves and aisles'.