Clan Macpherson enjoyed amicable relations with many of its neighbouring clans, although its policy of independence presented it with the enduring problems. The excellent relationship with the Clan Grant has also been explained but the 'bond of combination' for mutual protection signed in 1645 by the two clans during the Montrose campaigns is worth emphasising. Later Sir Aeneas of Invereshie urged his chief, Duncan of Cluny "to enter into a confederacy with some of the neighbouring clans" such as the Laird of Grant "because he is your nighest neighbour, his friends and yours have now for several ages drunk from the same stream, always been of one mind."
Such agreements took the form of a 'Bond of Friendship' which was intended to provide protection but also capable of producing a "confederacie" for insurgent action. In December 1691 when the plot to extirpate the MacDonalds of Glencoe was being hatched by the government of William III, Duncan of Clunie, Sir Aeneas and William Macpherson of Nuide signed a 'Mutual Contract of Friendship' with Alexander MacDonell of Glengarry to continue "the mutuall love, amitie and friendship that for several ages has so inviolable maintained betwixt their predecessors and families."
Another such agreement was the famous "Bond of Friendship between the Frasers, the Camerons, and the Macphersons" signed at Beaufort, the home of Simon Fraser, Lord Lovat, on the occasion of the marriage of Ewan Macpherson of Cluny to Janet Fraser in 1742. This confederation played an important part in the Rising of 1745 by laying the framework for Lovat's wish that the three clans "should be more unite and live together like brethren." The presence of entire units of Macphersons in the Fraser Highlanders at the capture of Quebec in 1759 and their later contribution to the Cameron Highlanders is apt testimony to the strong and continued attachment of the three clans in later decades of the 18th and early 19th centuries.
Relations with the Clan Mackintosh are more difficult to access due to the long-standing dispute over the chiefship of the Old Clan Chattan. There was no blood-feud over this issue nor did any Macpherson chief attempt to assert his authority over the other families who willingly followed the Mackintosh. The Macpherson chief's sole concern appears to have been independence within a loose confederacy. There is no evidence that the two clans tried to act together in matters of war and it appears that the two chiefs were often on opposite sides.
A clan with which the Macphersons were always on the best of terms was the Clan Gregor which was proscribed by King James VI and forbidden even to use their own surname for their defeat of the Colquhouns at the Battle of Glenfruin in 1603. In fact, the Macphersons might well have shared its fate, for a body of Badenoch clansmen was on its way to join the MacGregors when the battle took place. In 1611, it became legal to kill MacGregors and to hunt them with bloodhounds. An expedition of Camerons and Keppoch MacDonalds, bent on legal slaughter of fugitive Macgregors, was halted on the western bounds of the district by a force of 300 Badenoch men. As a result, Andrew of Cluny and two others were summoned to Edinburgh to appear before the Privy Council of Scotland and held in the Tollbooth prison for a month. In spite of this, the Macphersons were among those who provided asylum for the banished Griogaraich, some of whom were still living in Badenoch in the 19th century.