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Exile in England, 1549–1554

On his release, Knox took refuge in England. The Reformation in England was a less radical movement than its Continental counterparts, but there was a definite breach with Rome. The Archbishop of Canterbury, Thomas Cranmer, and the regent of King Edward VI, the Duke of Somerset, were decidedly Protestant-minded. However, much work remained to bring reformed ideas to the clergy and to the people. On 7 April 1549, Knox was licensed to work in the Church of England. His first commission was in Berwick-upon-Tweed. He was obliged to use the recently released 1549 Book of Common Prayer, which maintained the structure of the Sarum Rite while adapting the content to the doctrine of the reformed Church of England. Knox, however, modified its use to accord with the doctrinal emphases of the Continental reformers. In the pulpit, he preached Protestant doctrines with great effect as his congregation grew.

In England, Knox met his wife, Margery Bowes (died c. 1560). Her father, Richard Bowes (died 1558), was a descendant of an old Durham family and her mother, Elizabeth Aske, was an heiress of a Yorkshire family, the Askes of Richmondshire. Elizabeth presumably met Knox when he was employed in Berwick. Several letters reveal a close friendship between them. It is not recorded when Knox married Margery Bowes. Knox attempted to obtain the consent of the Bowes family, but her father and her brother Robert Bowes were opposed to the marriage.

Towards the end of 1550, Knox was appointed a preacher of St Nicholas' Church in Newcastle upon Tyne. The following year he was appointed one of the six royal chaplains serving the King. On 16 October 1551, John Dudley, 1st Duke of Northumberland, overthrew the Duke of Somerset to become the new regent of the young King. Knox condemned the coup d'état in a sermon on All Saints Day. When Dudley visited Newcastle and listened to his preaching in June 1552, he had mixed feelings about the firebrand preacher, but he saw Knox as a potential asset. Knox was asked to come to London to preach before the Court. In his first sermon, he advocated a change for the 1552 Book of Common Prayer. The liturgy required worshippers to kneel during communion. Knox and the other chaplains considered this to be idolatry. It triggered a debate where Archbishop Cranmer was called upon to defend the practice. The result was a compromise in which the famous Black Rubric, which declared that no adoration is intended while kneeling, was included in the second edition.

Soon afterwards, Dudley, who saw Knox as a useful political tool, offered him the bishopric of Rochester. Knox refused, and he returned to Newcastle. On 2 February 1553 Cranmer was ordered to appoint Knox as vicar of All Hallows, Bread Street, in London, placing him under the authority of the Bishop of London, Nicholas Ridley. Knox returned to London in order to deliver a sermon before the King and the Court during Lent and he again refused to take the assigned post. Knox was then told to preach in Buckinghamshire and he remained there until Edward's death on 6 July. Edward's successor, Mary Tudor, re-established Roman Catholicism in England and restored the Mass in all the churches. With the country no longer safe for Protestant preachers, Knox left for the Continent in January 1554 on the advice of friends. On the eve of his flight, he wrote:

Sometime I have thought that impossible it had been, so to have removed my affection from the realm of Scotland, that any realm or nation could have been equal dear to me. But God I take to record in my conscience, that the troubles present (and appearing to be) in the realm of England are double more dolorous unto my heart than ever were the troubles of Scotland.