For a few months after the Dissolution, the Abbey buildings stood empty in the hope of being the site for the cathedral for a new Dales bishopric. This was not to be, and by 1540 glass and lead from the dismantling of Fountains had found their way to Ripon and York.

The buildings and parts of the estate were sold to Sir Richard Gresham, whose family subsequently sold them on to Stephen Proctor, the builder of Fountains Hall. Then the abbey passed through several hands until it came into the possession of the Messenger family. In 1767 it was sold for £18,000 to William Aislabie, who landscaped the abbey ruins as a picturesque folly to be viewed from the Water Garden.