Sailing to join the rebel army on board the sloop Hound, he fought with his father's clan at the Battle of Falkirk, leading the Cromartie's Regiment of about 500 clansmen in the Jacobite rising of 1745 during which he was taken prisoner, with his father and 218 others, on 15 April 1746 at Dunrobin Castle, by a party of the William Sutherland, 17th Earl of Sutherland's militia the day before the Battle of Culloden, in the last siege fought on the mainland of Great Britain.

On 20 December 1746 he was not brought to trial before the Commissioners, though he pleaded guilty to high treason, but received full pardon on 26 January 1748 on condition "that within six months of his 21st birthday he would convey to the Crown all his rights in the Earldom" which was not restored until the reign of Queen Victoria.

Narrative by John Mackenzie, Lord Macleod eldest son of the Earl of Cromartie., the only other person not to stand trial for treason and pardoned.

Leaving Scotland, Mackenzie initially lived in Berlin with Field Marshal Keith, who assisted him in obtaining a commission in the Swedish Army in 1750.

From 1779 he served with his regiment in the East Indies Campaign against Hyder Ali, joining the army under Major-General Sir Hector Munro assembled at St. Thomas Mount, Madras, in July 1780.