He instead travelled to South Africa 1881 to 1884, for health reasons, where he studied Arts and Divinity at the Theological College of the Dutch Reformed Church at Stellenbosch University.
He returned to Scotland to complete his degree at the University of Edinburgh eventually graduating with an MA in 1889.
In 1908 he returned to University of Edinburgh as Professor of Church History in place of Rev Prof Malcolm Campbell Taylor.
[2] In the same year he became a Director of the Royal Blind Asylum in Edinburgh and a Governor of Steill's Educational Trust.
They had one son, James Alexander Rudolph MacKinnon (b.1888) an advocate who later served as Sheriff Substitute for Forfarshire.