 In 1581 he was holding, with his wardenship, the prebend of Henstridge in Wells Cathedral, and in 1589 the third prebend in Canterbury Cathedral.Hovenden entered on his duties as Warden of All Souls while the college was striving to preserve its Catholic 'monuments of superstition' in the chapel from demolition, but in December 1573 the orders of the commissioners in the matter were too stringent to be any longer disobeyed.Hovenden exerted himself, however, to secure the profitable management of the college estates.