McGuinness was given the job of Youth team manager in 1961 and in June 1969 he became senior coach when Sir Matt Busby announced his retirement. He was appointed manager a year later, but held the post for just six months and returned to coaching the Reserves.

McGuinness left the club in February 1971 and spent four years in Greek football as coach of Aris Salonika, then Panachaiki Patras. He returned to England to manage York City.

A qualified physiotherapist, he had spells as manager with Hull City and Bury before retiring from football in 1992.