Kirkcaldy was knighted at Holyrood Palace by Mary, Queen of Scots on 8 February 1562 during the festivities at the wedding of the queen's half-brother Lord James Stewart and Agnes Keith. He opposed Queen Mary's marriage with Lord Darnley, and was associated with her half-brother, Lord James. now Earl of Moray, at the time of the Chaseabout Raid. For this defiance, he was forced for a short time to seek refuge in England. Returning to Scotland, he was an accessory to the murder of Rizzio, but he had no share in Darnley's assassination.