MacDonald graduated from the University of Aberdeen in 1845 with a master's degree in chemistry and physics. He spent the next several years struggling with matters of faith and deciding what to do with his life. His son, biographer Greville MacDonald stated that his father could have pursued a career in the medical field but he speculated that lack of money put an end to this prospect. It was only in 1848 when MacDonald began theological training at Highbury College for the Congregational ministry.