He was born in 1600, the son of John MacKenzie of the Gairloch, his family being an offshoot of the kin of the earls of Seaforth.
After being ordained by John Maxwell, Bishop of Ross, he served as a chaplain in a regiment of King Gustavus Adolphus of Sweden during the Thirty Years' War.
He returned from Germany to become parson (i.e. rector) of the parish of Contin in Ross, moving to take charge of the church of Inverness, and then taking over as minister of Elgin.
Following the Restoration and re-establishment of Episcopacy, MacKenzie was selected to be the new Bishop of Moray on 18 January 1662.
He married Margaret MacLey the daughter of Dòmhnall Mac an Lèigh (Anglicised: Donald McLey), bailie of the burgh of Fortrose.