In 1645 Leslie was sent back to Scotland to deal with the Royalists there during the Scottish Civil War. He routed the main Royalist force under James Graham, Marquis of Montrose at the Battle of Philiphaugh (September 1645) and was rewarded by the committee of estates with a present of 50,000 merks and a gold chain; but his victory was marred by the butchery of the captured Irish—men, women and children—to whom quarter had been given. He was then declared lieutenant-general of the forces, and, in addition to his pay as colonel, had a pension settled on him. One of those captured at Philiphaugh was his old commanding officer, Alexander Leslie of Auchintoul, for whom he intervened personally to save from execution. Auchintoul was banished for life, leading to his return to Russia.