The church has a continuous nave and chancel—all of one height—under a single thatched roof. The chancel dates to c.1300. An aisle was added on the south side of the nave in the 14thc and a square tower at the W end in the 15th. A programme of refurbishment took place in 1865. Two circular double-splay windows high up in the N wall indicate that the nave dates partly to the 11thc, although the font at the W end of the building is now the only Romanesque sculpture in the building.

At the Norman Conquest, Stigand, Archbishop of Canterbury had holdings in Coltishall. A church 'with ten acres' is mentioned there in Domesday Book. The present church was dedicated to St John the Baptist in 1284 but it conserves the structure of a building that is at least two centuries older. This may have been the ‘mother church’ referred to in the resolution of a dispute of c.1146 x 1145 between its priest, William, and Herman, clerk of the chapel of Hautbois, who was to receive all customary tithes and offerings apart from ‘Wachecroft.’ This was to be rendered to Coltishall, together with an annual pension from Hautbois of 10 shillings. Burials were to take place only at Coltishall, the ‘mother church’, but the burial dues were to be shared equally with Hautbois.

Four-sided dark marble font basins very similar to this, with incised or low-relief blank arcading, are found elsewhere in the county, for example at Thorpe-next-Haddiscoe, Horsford, Woodton and Reepham.