His father, James V, wrote to Cardinal Rodolfo Pio da Carpi, in July 1541 that John should be Prior of Coldingham in place of Adam Blackadder, who became Abbot of Dundrennan, and his son would be able to prevent Protestant doctrine spreading from the nearby border with England.
[4] In 1550, after the conclusion of the war known the Rough Wooing, he accompanied his step-mother Mary of Guise on a visit to the French court.
[6][7] In April 1558 he wrote to Mary of Guise from Coldingham about a dispute amongst his tenants in Glasgow who were now threatened with legal action by Robert, Lord Sempill, as Sheriff of Renfrew.
[8] During the Reformation Crisis the English government sent a fleet of warships to Scotland, and subsequently, by the Treaty of Berwick, an army to assist the Protestants at the siege of Leith.
In January 1560 John Stewart sighted the English fleet commanded by William Wynter off Dunbar sailing towards the Isle of May and sent a boat to investigate.
The English diplomat Thomas Randolph wrote that Lord John was in the queen's favour in October 1561, for his "leaping and dancing", and would marry the Earl of Bothwell's sister, Jean Hepburn.
While Kirkcaldy was talking to the porter, the castle watchman on the tower spotted Coldingham and the Master of Lindsay and their troops a mile off.
He alerted the Earl, who hopped over a low wall at the back of the castle and found a horse before Pitcur could stop him.
Elizabeth Keith, Countess of Huntly then welcomed the queen's men in and gave them a meal and showed them around the place.