Around 1200, a new parish church was built in St Neots,possibly on the site of the original Priory, while had moved to a stone structure by the river to the north of the Market.
Because the Priory was an 'alien house', that is, it belonged to a French order, it suffered from intermittent confiscations during the Hundred Years' War from 1338, as well as the payment of an annual fee which amounted to over half their annual income.