Although the Clan was predominantly royalist (and later on, Jacobite) it was also represented on the side of the Commonwealth. Dougal Macpherson of Powrie (a member of the Ballachroan family) was commander of Blair Castle in 1644 and captain of Ruthven Castle in 1648. He was also joint commander (with Locheil and Mackintosh) of Argyll's forces in Badenoch and bailie of Badenoch for Argyll in 1650.
In 1662, after Charles II was restored to the throne in England, John Macpherson of Dalraddie, a brother of William of Invereshie who died of wounds sustained while fighting for Montrose at Auldearn, and Ewan Macpherson, tutor and legal guardian to the young chief Andrew of Cluny, were both fined £600 for their adherence to the Commonwealth.