As bishop, Pilkington sought to bring order to his diocese, dealing with recusancy and conflicts of power with the Earls of Westmorland and Northumberland, in which he was helped by the new dean, William Whittingham, appointed in 1563. Pilkington and Whittingham worked to ensure the appointment of committed reformers in what had been an area of strong recusant Roman Catholic feeling. In the 1560s and 1570s Pilkington exercised his patronage of cathedral prebends and invariably nominated zealous Protestants, many of them his relatives and friends.