When Thomas Cranmer was brought to the stake to be burnt at Oxford, he took leave of some of his friends standing by, and seeing Ely among them went to shake him by the hand, but the latter, drawing back, said it was not lawful to salute heretics, especially one who falsely returned to the opinions he had forsworn.
In 1559 he was appointed the second president of St John's College, Oxford, by Sir Thomas White, its founder, but about 1563 he was removed from that office on account of his refusal to acknowledge the supremacy of the queen over the church of England.
At length being apprehended he was committed to Hereford gaol, where he spent the remainder of his life.
In a report sent to the privy council in 1605 the high sheriff of Herefordshire says: "Mr. Elie, a prisoner there [at Hereford], is a setter forward of their [the jesuits'] desperate designs with all his might, having such liberty as that he rideth up and down the country as he listes."
Dodd says that "his years and strictness of his morals made him both fear'd and respected, not only by those of his own persuasion, but by most others: who never durst utter anything unbecoming a christian in his presence."