Born in Inverness County, Cape Breton Island, Nova Scotia, the son of Finlay and Catherine (Beaton) MacDonald, MacDonald was educated in the common schools of Inverness County and attended St. Francis Xavier College (now St. Francis Xavier University) in Antigonish, Nova Scotia.

In 1879, he went to Rome and studied philosophy and theology at the Propaganda College graduating in 1884.

He was ordained in St. John Lateran church in Rome, by Lucido Maria Cardinal Parocchi on March 8, 1884.

In 1884, he returned to back to Nova Scotia where he was appointed teacher of Latin and philosophy at St. Francis Xavier College.

In 1900, he was appointed vicar general of his diocese and three years later was given charge of St. Andrew's parish in Antigonish County, Nova Scotia.