In 1553, when Mary I became Queen, Aylmer fled to the Continent where he made contact with the European Protestant reformers. When Elizabeth ascended the throne, he returned to England where he became the Archdeacon of Lincoln.

In 1566 Aylmer was consecrated Bishop of London. He died in 1594 and was buried in Old St. Paul's.

Aylmer wrote "A Harbour for Faithful Subjects" in which he gives the following account of Jane's piety;

'The King left her [Princess Elizabeth] rich cloths and jewels; and I know it to be true, that in seven years after her father's death, she never in all that time looked upon that rich attire and precious jewels but once and that against her will. And that there never came gold or stone upon her head, till her sisiter forced her to force off her former soberness, and bear her company in her glittering gayness. And then she so wore it, as every man might see that her body carried that which her heart misliked. I am sure that her maidenly apparel which she used in King Edward's time, made the noblemen's daughters and wives to be ashamed to be dressed and painted like peacocks; being more moved with her virtuous example than with all that ever Paul or Peter wrote touching that matter. Yea, this I know, that a great man's daughter [Lady Jane Grey] receiving from Lady Mary before she was queen, good apparel of tinsel, cloth of gold and velvet, laid on with parchment lace of gold, when she saw it, said; 'What shall I do with it?' 'Marry,' said a gentlewoman,' wear it.'