The 1990s saw Alan Shearer emerged as an exciting prospect at the club and in 1992 Saints reached the Zenith Data Systems Cup Final at Wembley, going down 3-2 to Nottingham Forest in extra-time after an epic battle. Shearer was Saints' top scorer with 21 goals and was capped by England.
On the eve of the 1992/93 season an English record transfer fee of £3million saw Blackburn Rovers prise Shearer away from the south coast and Saints were amongst the teams in the newly formed Premier League. Tim Flowers followed his former team-mate to Lancashire mid-way through the 1993/4 season,
1996/97 saw the arrival of Scotland hero Graeme Souness as manager.
Souness brought in several new players including centre-back Claus Lundekvam and, despite masterminding a 6-3 annihilation of Manchester United, for the third time in four years Saints were not safe until the final day when they stayed up despite a 1-0 defeat at Aston Villa.