As a priest and a notary in 1540, Knox tutored two sons of Hugh Douglas of Longniddry and the son of John Cockburn of Ormiston who embraced the new religious ideas of the Reformation.
Knox became the bodyguard of George Wishart, a reformer who had returned to Scotland. In 1545, Wishart was arrested and taken to the Castle of St Andrews at the behest of Cardinal Beaton.
Knox and his pupils became fugitives, but came to the Castle of St Andrews, after the Cardinal’ murder. He considered the Bible as his sole authority and the Pope Antichrist
Knox's chaplaincy ended when the French besieged the castle and took him and others as galley slaves. In February 1549, after spending a total of 19 months in the galley-prison, Knox was released
He took refuge in England where The Archbishop of Canterbury, Thomas Cranmer, and the regent of King Edward VI, were Protestant-minded. From his pulpit in Berwick-upon-Tweed, he preached Protestant doctrines as his congregation grew.
Appointed preacher of St Nicholas' Church in Newcastle, in1551, he was appointed as a royal chaplains serving the King. When John Dudley, 1st Duke of Northumberland, overthrew the regent, he condemned the coup d'état.
Knox was summoned to London to preach before the Court. There, he opposed idolatry and the practice of kneeling during communion. A compromise was reached with Black Rubric stating no adoration is intended while kneeling.
After Edward’s death in1554, he fled to Geneva and met French theologian John Calvin. He condemned Mary Tudor, Edward’ successor and accepted an invitation from a congregation of English exiles in Frankfurt.
Richard Cox, one of the authors of the Book of Common Prayer, brought Knox's pamphlet attacking the emperor to the attention of the Frankfurt authorities, who advised him to leave in 1555
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He returned to Scotland in 1555 and preached for nine months the reformed doctrines. Welcomed by the nobility and regarded as a threat by the bishops, he was forced to return to Geneva.
He returned to Scotland in 1559, and within days of his arrival, he preached a violent sermon at Perth (Scotland) against Catholic "idolatry," causing a riot which he condemned
The Protestants in Perth rebelled against the regent, who advanced with her troops from Stirling. A parley with the Congregation resulted in a treaty and the Protestants were to be allowed complete freedom of worship.
He next moved to St. Andrews, Stirling, and finally marched to Edinburgh, while the regent retreated to Dunbar and in 1559 he was chosen minister of the Edinburgh Protestants.
The Protestants militarily occupied more cities and by the Treaty of Berwick (1560), the English now under Protestant Elizabeth I, and the French, agreed to leave Scotland assuring the future of Protestantism in Scotland
The Parliament ordered Knox and five colleagues to write a Confession of Faith, the First Book of Discipline, and The Book of Common Order—Protestant faith was cast in a distinctly Calvinist mode.
In 1558, Knox published, First Blast of the Trumpet Against the Monstrous Regiment of Women, a polemical treatise against female sovereigns and their policies, but also against female rule over men generally.
The History of the Reformation in Scotland is a magnum opus written by Knox between 1559 and 1566. It has been used as an historical source since its full publication