Immediately after joining United, Donaghy was the club's first-choice left-back for the 1988–89 season, missing only the League Cup game for which he was cup-tied. However, his opportunities were limited in the 1989–90 season, and he was unable to make even the substitutes bench for the 1990 FA Cup Final triumph over Crystal Palace. However, he did make the substitutes bench for the European Cup Winners' Cup triumph in 1990–91.