St Neots Priory was no exception and was forced to close in 1539, the remaining 12 monks being pensioned off. Eight years later, the buildings and land were sold while the manor was given to the King’s daughter Elizabeth, later to become Queen Elizabeth I.
In 1591, there were 879 people living in Eaton Socon; as Eynesbury and St Neots may both have been a similar size, this suggests a total population of at least 2000. St Neots Grammar School was in existence by 1556 when the schoolmaster was a Mr Faucet. The Priory buildings fell into a state of disrepair, but were still at least partly standing in 1584.
In 1588, a new bridge was built, mainly wooden but with masonry piers in the river. Possibly some of this stone was salvaged from the ruins of the Priory.