Beaton became archbishop of St. Andrews in 1539 and papal legate in Scotland in 1544. Beginning his political career in 1529, he eventually became the trusted counsellor of King James V. He dissuaded the King from following the Reformist religious policies of Henry VIII of England and helped arrange James's two successive marriages to French noblewomen. After James's death in 1542, Beaton's opposition to the pro-English policies of James Hamilton, 2nd earl of Arran—regent for James's daughter, Mary Stuart—led to his imprisonment from January to April 1543. After Arran changed sides, Beaton became chancellor and virtual ruler of Scotland and initiated a persecution of Protestants. By blocking the proposed marriage of Mary Stuart to the future king Edward VI of England, he frustrated Henry's design for the subjugation of Scotland and provoked the abortive English invasion of 1544.

Beaton had the popular reformer George Wishart (Wishart, George) burned at the stake on March 1, 1546, and in revenge a band of Protestant nobles, possibly at the behest of Henry VIII, murdered him in St. Andrews Castle.