On 9 November 1594, soon after his father's death, Mackenzie made oath in presence of the King and the Privy Council that he would "faithfully, loyally, and truly concur, fortify, and assist his Majesty's Lieutenant of the North with his advice and force at all times and occasions as he may be required by proclamations, missive letters, or otherwise."
He proved himself to be a masterful political operator but even he had to deal with potentially serious setbacks and the Privy Council's records show that he was on at least one occasion imprisoned in Edinburgh Castle.
Although he was raised to the peerage on 19 November 1609, by the title of Lord Mackenzie of Kintail, he was not so designated in the Privy Council Records until 31 May 1610, when the patent of his creation was read and received by their Lordships, and he was thereupon acknowledged to be a free baron in all time coming.
At a meeting of the Privy Council, held at Edinburgh on 30 September 1605, Mackenzie received a commission to act for the King against Neil MacNeill of Barra, the Captain of Clanranald, and several other Highland and Island chiefs, who had "of late amassed together a force and company of the barbarous and rebellious thieves and limmers of the Isles," and with them entered Lewis, "assailed the camp of his Majesty's good subjects," and "committed barbarous and detestable murders and slaughters upon them."
Mackenzie received another commission in Lewis on 1 September 1607 against Neil Macleod, another of Old Ruari's sons, who was conducting a guerilla campaign against the Fife adventurers and had recently captured the Castle of Stornoway.
By covert support for local resistance, Mackenzie once again skilfully undermined their campaign to assert their rights, with the eventual result that they sold them to him for a substantial sum and a lease of his woods at Letterewe.
A commission of fire and sword was granted to Mackenzie against him and all his followers, with a decree of ransom for the loss of those who were burnt and plundered by him, and for Kintail's charges and expenses, making altogether a very large sum.
Armed with his commission and accompanied by a large force, Mackenzie defeated Macdonell at Morar and drove back to Kintail "the largest booty ever heard of in the Highlands of Scotland".
A cousin of his, Allan Dubh MacRanuil of Lundie committed one further great atrocity when he burned the church of Kilchrist in Easter Ross, killing the congregation gathered inside.
However, the Macdonells, despite their sanguinary excesses, were no match for the politically astute Mackenzie, who (in 1607) succeeded in obtaining a crown charter to the disputed districts of Loch Alsh, Lochcarron and others, and who steadily bought up the claims of third parties against Glengarry.