Tunstall disliked the religious policy pursued by the advisers of King Edward VI, and voted against the first Act of Uniformity in 1549. However, he continued to discharge his public duties without interruption, and hoped that the Earl of Warwick might be induced to reverse the anti-Catholic policy of the Duke of Somerset. This hope failed, and after Somerset's fall, Tunstall was summoned to London in May 1551, and confined to his house there. During this captivity he composed a treatise on the Eucharist, which was published at Paris in 1554. At the end of 1551 he was imprisoned in the Tower of London, and a bill for his deprivation was introduced into the House of Commons. When this failed, he was tried by a commission on 4–5 October 1552, and deprived of his bishopric.