structural:expansion
Return to Geneva, 1556–1559

Shortly after Knox sent the letter to the Queen Regent, he suddenly announced that he felt his duty was to return to Geneva. In the previous year on 1 November 1555, the congregation in Geneva had elected Knox as their minister and he decided to take up the post. He wrote a final letter of advice to his supporters and left Scotland with his wife and mother-in-law. He arrived in Geneva on 13 September 1556.

For the next two years, he lived a happy life in Geneva. He recommended Geneva to his friends in England as the best place of asylum for Protestants. In one letter he wrote:

I neither fear nor eschame to say, is the most perfect school of Christ that ever was in the earth since the days of the apostles. In other places I confess Christ to be truly preached; but manners and religion so sincerely reformed, I have not yet seen in any other place...

Knox led a busy life in Geneva. He preached three sermons a week, each lasting well over two hours. The services used a liturgy that was derived by Knox and other ministers from Calvin's Formes des Prières Ecclésiastiques. The church in which he preached, the Église de Notre Dame la Neuve —now known as the Auditoire de Calvin —had been granted by the municipal authorities, at Calvin's request, for the use of the English and Italian congregations. Knox's two sons, Nathaniel and Eleazar, were born in Geneva, with Whittingham and Myles Coverdale their respective godfathers.

In the summer of 1558, Knox published his best-known pamphlet, The first blast of the trumpet against the monstruous regiment of women. In calling the "regimen" or rule of women "monstruous", he meant that it was "unnatural". Knox states that his purpose was to demonstrate "how abominable before God is the Empire or Rule of a wicked woman, yea, of a traiteresse and bastard". The women rulers that Knox had in mind were Queen Mary I of England and Mary of Guise, the Dowager Queen of Scotland and regent on behalf of her daughter, Mary, Queen of Scots. This biblical position was not unusual in Knox's day; however, even he was aware that the pamphlet was dangerously seditious. He therefore published it anonymously and did not tell Calvin, who denied knowledge of it until a year after its publication, that he had written it. In England, the pamphlet was officially condemned by royal proclamation. The impact of the document was complicated later that year when Elizabeth Tudor became Queen of England. Although Knox had not targeted Elizabeth, he had deeply offended her, and she never forgave him.

With a Protestant on the throne, the English refugees in Geneva prepared to return home. Knox himself decided to return to Scotland. Before his departure, various honours were conferred on him, including the freedom of the city of Geneva. Knox left in January 1559, but he did not arrive in Scotland until 2 May 1559, owing to Elizabeth's refusal to issue him a passport through England.