Watson was an integral part of the Everton side throughout the 1990s, and following the departure of goalkeeper Neville Southall in 1998 he became the club's oldest and longest serving player. However, the 1990s were a generally unsuccessful decade for Everton after the glories of the 1980s. They did finish sixth in 1990 after topping the table earlier in 1990–91, but then endured four seasons of mid table finishes, and avoided relegation in 1994 on the last day of the season. Watson got his hands on some silverware for one final time in 1995 when he captained Everton to a surprise 1–0 win over Manchester United in the FA Cup final – by now he was one of the last players remaining from Everton's last major trophy win (the league title) eight years earlier. He was man of the match for that game.