He was succeeded in the peerages by his eldest son, the second Earl. On his death, the titles passed to his eldest surviving son, the third Earl. He supported the Jacobite rising of 1745 and led a force of 400 men from Clan Mackenzie at the Battle of Falkirk in 1746. Lord Cromartie was captured by government forces the same year and pleaded guilty to high treason before the House of Lords. He was sentenced to death but received a conditional pardon on 22 January 1748, on the condition that within six months he surrender all the rights of his estates as lord and forfeit his titles, which he did. His eldest son and heir apparent, John Mackenzie, Lord MacLeod, fought alongside his father in the rebellion of 1745. He was also convicted of high treason and sentenced to death, but received a full pardon in 1748. He later had a successful career in both the British and Swedish armies. He achieved the rank of Major-General in the British Army, and was created a Count in the Swedish nobility, a title which was recognized by George II. In 1784,the Cromartie estates were restored to him by Act of Parliament for a payment of £19,000 (). Lord MacLeod died childless in 1789, and in his will he created an entail as to his heirs.