He is believed to have had a hand in suppressing the rebellion of John Macdonald, 11th Earl of Ross, the last of the Lords of the Isles.
According to 18th century historian William Guthrie, John Stewart, Earl of Atholl was killed at the Battle of Flodden in 1513.
However, the exact number, names, and the attribution of his children to their mothers is unclear.
She died between 1473 and 1475. and they had two daughters: Sometime before April 1475, he married as his second wife, Lady Eleanor Sinclair (died 21 March 1518), daughter of William Sinclair, 3rd Earl of Orkney and Marjory Sutherland.
They had two sons and nine daughters: According to legend, the Earl of Atholl had whisky, honey and oats added to Macdonald's water well, which so entranced or intoxicated him that Macdonald was easily captured.