Created a baronet in 1642 for his services, he was excommunicated and forced to surrender by the Covenanters under Argyll at Kellie in 1644 and was subsequently beheaded for treason at Edinburgh.
Huntly was forced to retreat, but Sir John tried to hold Kellie against a powerful army led by the "glied Argyll".
[1] He joined the Marquis of Huntly in behalf of the king, and sentence of excommunication was pronounced against them both by order of the committee of the general assembly on 16 April 1644.
Promised honourable terms of surrender by his cousin, Earl Marischal, then in Argyll's army, Gordon capitulated unconditionally on 8 May 1644.
Argyll released most of the garrison, but held Gordon and a few officers and plundered Kellie in violation of his terms, much to Marischal's dissatisfaction.