The citizens of Medehamstede, lived to the east of the abbey and what is now the Cathedral, on the edge of the fenland. After the great fire of 1116, the inhabitants were moved to the west of the abbey where the land was drier. Unfortunately they did not move the church to the west, and for several centuries the inhabitants of the town had to walk round the vast abbey grounds to reach their isolated church. This was made more difficult by flooding from streams that ran in front of the church, making attendance problematic in the winter.
A petition was made to move the church to the west of the abbey, which was granted by the Bishop of Lincoln in 1402. The new church was built using stone from the old one and the Becket Chapel, as well as oak from Abbot William Genge's park. He dedicated the church to St John the Baptist on 26th June 1407.
It was originally built with a large leaded spire, which was conspicuous from some distance. Unfortunately, due to instability, it was removed in the 1820s, but it can be seen in John Speed's Map, A Prospect of Peterborough and an old photograph.