A premature expression of Lutheran views is said to have caused his departure from Oxford and even his imprisonment, but the records are silent on these sufferings which do not harmonise with his appointment as Master of the Royal Foundation at Eton.
In 1540 he was one of the fifteen divines to whom were referred crucial questions on the sacraments and the seat of authority in the Church; his answers (printed in Pocock's Burnet, iii.
Moreover, he was present at the examination of Robert Barnes, subscribed the divorce of Anne of Cleves, and in that year of reaction became Archdeacon and Prebendary of Ely and Canon of Westminster.
In December, he was appointed Dean of Oseney (afterwards Christ Church) Oxford, and in July was made Almoner to Prince Edward, in whose education he took an active part.
The exiles had, under the influence of John Knox and William Whittingham, adopted Calvinistic doctrine and a form of service far from the Prayer Book of 1552.
He was an honest, but narrow-minded ecclesiastic, who held what views he did hold intolerantly, and was always wanting more power to constrain those who differed from him (see his letter in Hatfield MSS.
While he refused to minister in the Queen's Chapel because of the crucifix and lights there, and was a bitter enemy of the Roman Catholics, he had little more patience with the Puritans.
The Queen herself intervened, when he refused to grant Ely House to her favourite, Sir Christopher Hatton; but the well-known letter beginning "Proud Prelate" and threatening to unfrock him seems to be an impudent forgery which first saw the light in the Annual Register for 1761.
Cox died in July 1581; a monument erected to his memory twenty years later in Ely Cathedral was defaced, owing, it was said, to his evil repute.