Mackenzie was only 14 when his father died in 1611, and the clan territories were therefore entrusted to his uncle, Sir Roderick Mackenzie of Coigach, the Tutor of Kintail. Upon Lord Mackenzie's death, Neil Macleod and other members of the Macleods of Lewis, whom Lord Mackenzie had recently subdued, rose in rebellion in Lewis. A number of commissions against them were granted between 1611 and 1616 to the Tutor of Kintail, Colin Mackenzie of Killin, Murdo Mackenzie of Kernsary, Alexander Mackenzie of Coul and Kenneth Mackenze of Davochmaluag, while neighbouring chiefs (Donald Gorm Macdonald of Sleat, Roderick Macleod of Harris, Hugh Mackay of Farr and his son, and MacNeill of Barra) were forbidden to assist the rebels. Neil Macleod himself was captured and executed in Edinburgh in April 1613, but the turbulence continued. By a special commission from the king dated 14 September 1614, the Mackenzies were exempted by reason of their involvement in Lewis from engaging in the resolution of a dispute between two factions of the Clan Cameron (acting as proxies for the Marquis of Huntly and the Earl of Argyll). Once it had again eventually been brought under control, Lewis remained in the possession of the Mackenzies of Kintail until it was sold to Sir James Matheson in 1844.