In July 1596, upon paying a sum of money into the royal treasury, he received a commission as the King's lieutenant in the bounds of Clan Gregor "wherever situated".

[3] In 1602 the MacGregors began to make more formidable inroads into the lands of Luss and Colquhoun of Luss complained to King James VI of Scotland who despite having passed an Act of Parliament forbidding the carrying of arms, granted permission to Colquhoun and his tenants to wear various offensive weapons.

However, the right granted to Colquhoun and his followers to carry arms seems to have caused resentment from the MacGregors and resulted in the conflicts at both Glenfinlas and Glen Fruin.

When the two were discovered they were seized and brought forward to Colquhoun, the Laird of Luss who had the men tried by summary trial and then executed.

He granted a commission of lieutenancy to Colquhoun of Luss giving him the power to repress the crimes made against him and to apprehend the perpetrators.

Fraser states that at this time the town council of Dumbarton issued an order for the burgesses to be provided with weapons and armour in readiness, no doubt, for the Clan Gregor.

To repel the invaders Colquhoun gathered together a considerable force of armed men, who under the royal commission, he had raised to protect the district and punish the MacGregors.

Meanwhile, his brother, John MacGregor, with the ambush division took a detour to the rear of the Colquhouns which prevented their retreat back through the glen without fighting their way through.

However, due to the unfavorable circumstances in which they had to fight, the Colquhouns were unable to maintain their ground and fell into the moss at the farm of Auchengaich where they were thrown into disorder.

[10] King James sought to make the Highlands and Islands "answerable to God, justice and himself" and to assimilate them into his new Britain.

[7] There is a tradition that after the battle the victorious MacGregors slaughtered a group of clerical students who had come to watch it, but this story is not supported by historical records.

[16] It is alluded to in the supposed factual introduction to Walter Scott's novel Rob Roy in which it says that the culprits were from the Clan MacFarlane, allies of the MacGregors.

[17] According to John Parker Lawson, there is a story that a group of theological students who had come to witness the battle but who were probably on an excursion at the time had been put into a barn for safety by the chief of Colquhouns.

[19] The writer Peter McArthur composed a ballad entitled The Raid of Glen Fruin in memory of the battle.

There is also a grey stone in the glen where it is believed that John MacGregor, the chief's brother, who was one of the few slain on the other side was buried.