Gordon was the son of George Gordon (d. 1610), by Margaret, daughter of Sir Alexander Bannerman of Elsick in Aberdeenshire. He succeeded his grandfather, James Gordon of Methlick and Haddo, Aberdeenshire, in November 1624. In 1639, Gordon was appointed by
Charles I second-in-command of the forces raised against the Covenanters, under the
Marquess of Huntly. He took a distinguished part in the skirmish at
Turriff on 14 May 1639, where the Royal forces dispersed a gathering of the Covenanters. Gordon was made a
baronet on 13 August 1642 for his role in this affair, an honour which rendered him further odious to the Covenanters. After the conclusion of the treaty of pacification on 20 June, Gordon repaired to the king at Newark. When Huntly raised an army for the King that year, Sir John again joined him, and both were excommunicated by the General Assembly in April. Huntly was forced to retreat, but Sir John tried to hold Kellie against a powerful army led by the "glied
Argyll". For his opposition to the covenant, letters of intercommuning were issued by the convention against him in November 1643, and an order granted for his apprehension. The sheriff of Aberdeen proceeded accordingly, in January 1644, to his house of Kellie at the head of a large force, but Gordon had escaped. Gordon was brought to
Edinburgh and imprisoned in the western part of
St. Giles' Cathedral, which thereby acquired the name of "Haddo's Hole". He was tried for
high treason against the Estates for his actions in 1639, and for maintaining a garrison against the Covenanting armies. Gordon defended himself on the grounds that his actions at Turriff had been pardoned under the Pacification of Berwick, and that he had had the King's authority in his deeds, to no avail. He was found guilty and beheaded at the
Mercat Cross in Edinburgh on 19 July 1644. ==Family==