The founder of the MacKintosh clan is reputed to have been Shaw MacDuff, second son of the Earl of Fife, and a member of the royal house of Dalriada. He travelled north with Malcolm IV in the twelfth century to suppress rebellion in Morayshire and was granted lands in the Findhorn valley. These lands became the heartland of the clan and the burial place of the clan chiefs.

Shaw was known at this time as "Mac an Toiseach" or "son of the chief", hence the name MacKintosh. The MacKintosh chiefs steered themselves through the hazards of Scottish history with great skill, even leading the great confederation of clans known as Clan Chattan, although this honour was challenged by the MacPherson chiefs on many occasions over the centuries.

The MacKintosh clan had to fight to defend their powerful position and conducted long-running feuds with the Earls of Moray and Huntly, among others.