Macdonald enrolled in The Queen's Own Rifles of Canada on 13 October 1868 as a Rifleman. He spent the summer of 1866 with the 14th Battalion Volunteer Militia Rifles near Cornwall, in anticipation of a Fenian invasion. He rose to the rank of Sergeant before being commissioned as an Ensign on 22 April 1870. Macdonald then joined the expedition of Colonel Garnet Joseph Wolseley and made the trek to the Red River settlement in Manitoba. The Wolseley Expedition was formed to put down Louis Riel's Red River Rebellion. After taking part in the bloodless capture of Upper Fort Garry (after Riel's departure) he returned to Toronto, but would take part in putting down Riel's second rebellion. He retired from the QOR on 26 April 1882 and moved to Winnipeg. During the North-West rebellion in 1885, Macdonald served as a lieutenant in the 90th (Winnipeg) Battalion of Rifles, a unit which he helped to organize. He later fought at Fish Creek in Saskatchewan.