In 1823 he became assistant to Robert Jameson, the Regius Professor of Natural History at the University of Edinburgh.

He died at 67 Crown Street[3] in Aberdeen on 5 September 1852 but is buried in New Calton Cemetery in Edinburgh.

His eldest son, John MacGillivray (1822–1867), published an account of the voyage round the world of HMS Rattlesnake, to which he was the onboard naturalist.

Another son, Paul, published an Aberdeen Flora in 1853, and donated 214 of his father's paintings to the Natural History Museum.

A detailed version of MacGillivray's life, written by a namesake, was published 49 years after the ornithologist's death.