In December, 1545, he was seized and then transferred to Edinburgh Castle, and then delivered to Cardinal Beaton, one of the great persecutors of the Reformers in Scotland, and was placed in St. Andrew's Castle. After a mock trial he was sentenced to be burnt. He was killed in front of St. Andrew's Castle on March 1st, 1546. As he was burning, seeing Cardinal Beaton sitting in the castle watching his execution, he said, “He who sits in such state, from that high place, feedeth his eyes with my torments, within a few days shall be hanged out at the same window to be seen with as much ignominy as he now leaneth there in pride.”1 This prophesy was fulfilled just two months later when he was killed in the same castle by some conspirators who desired to revenge Wishart's death.
1 As quoted in As quoted in J. H. Merle D'Aubigne, History of the Reformation in Europe in the Time of Calvin (Harrisonburg, VA: Sprinkle Publications, 2000) volume 3, book x, p. 206