The sentence passed on Kirkcaldy for his share in Beaton's murder was removed in 1556. Returning to Scotland in 1557 he became prominent by killing Ralph Eure the brother of the Governor of Berwick upon Tweed in a duel. As a Protestant he was one of the leaders of the Lords of the Congregation in their struggle with the Regent of Scotland, Mary of Guise. Kirkcaldy fought the French troops in Fife and they destroyed his house at Halyards. In January 1560 he took down part of Tullibody bridge to delay the return to Stirling of French troops commanded by Henri Cleutin.