During the Sixteenth Century Reformation, Winchelsea’s Dominican and Franciscan endowments were confiscated and later pulled down, including the hospitals.
On the accession of Queen Mary in 1547, the rector Peter Danyell was deprived of his living and replaced by the Catholic Robert Jordan. Danyell was reinstated on the accession of Queen Elizabeth in 1559.
During these turbulent years the interior of the church fell into a deplorable state of repair, made worse by the decline of trade due to the silting up of the town’s harbour and, possibly, to damage by Puritan iconoclasts. By the 1660s the diarist John Evelyn wrote of the ‘forlorn ruins’ he found in Winchelsea.