In the rest of McAllister's time at Leeds, the highest the club finished was fifth in the 1993–94 and 1994–95 seasons. The lowest was 17th in the 1992–93 Premier League – one of the lowest-placed finishes of a defending league champion in English football history. He captained the side for two seasons. During the 1992–93 season, McAllister made his debut in the UEFA Champions League. He scored in matches against VfB Stuttgart and Rangers, but Leeds were knocked out by the latter in a match hyped as the "Battle of Britain". In McAllister's final season Leeds finished 13th. He captained the team at Wembley Stadium in the 1996 League Cup Final, where they were beaten 3–0 by Aston Villa.