Macqueen was a Church of Scotland minister in the Isle of Skye and a notable scholar. He was born in Trotternish, the son of the Rev. Archibald Macqueen (1671-1754), Minister of Snizort and Uig, and Isabella Mackenzie (d. 1718). He was married twice, firstly (1744) to Betsy Martin, and secondly (1749) to Anne Macdonald (d. 1756). Father of John Macqueen, Minister of Applecross. Among his descendants were Thomas Potter Macqueen, who sat as Member of Parliament from 1816 to 1830.
Macqueen was appointed minister of Kilmuir and Kilmaluag on the Trotternish peninsula of Skye in 1740. He was highly regarded by his contemporaries, and according to the Fasti Ecclesiae Scoticanae was probably the best known and most distinguished minister in the Highlands in his own time. He was the author of several works, including Reflections on Clanship (1763) and Dissertation of the Government of the People of the Western Isles (1774). Late in life, in 1781 he was admitted as a corresponding member of the Society of Antiquaries of Scotland.
Donald Macqueen died in 1785 on the isle of Raasay, and he is buried in Kilmuir churchyard.
Boswell and Dr Johnson met Macqueen on the coast of Skye near Broadford on September 8, 1773, when he arrived to accompany them on their crossing to the isle of Raasay. Boswell instantly took a liking to the old churchman, describing him as "a decent minister, an elderly man with his own black hair, courteous and rather slow of speech, but candid, sensible, and well-informed, nay, learned."