It was probably whilst working on the restoration of Ely that Willis first began to study a monastic site, which posed a set of problems he had not previously encountered. By contrast with churches, whose basic function was well understood, conventual buildings appeared as ruined fragments of a lost way of life. The Romantic could conjure from the ruins the spectres of long-dead abbots and mad monks, but to the more ‘scientific’ observer, the standing stones remained all but illegible. A reviewer of Richard Warner's An History of the Abbey of Glaston (1826) thus compared the ruins unfavourably with complete edifices in the same style:

At Ely, what remained were not ‘mere pieces of wall’ but a few complete buildings and other fragments incorporated into post-Reformation structures. Most of the claustral complex had disappeared but Willis arrived in time to write an account of the Sextry barn (the barn belonging to the sacristan) for the Cambridge Antiquarian Society in 1843, the year after it too had been demolished.