The 1998- 1999 campaign proved to be a tough one for Bolton as their quest in searching for automatic promotion back in to the top flight was a failure, despite promise in reaching the play offs after a sixth place finish. They repeated their league performance the following season as they once again reached the sixth position; however, they were a dominant force in the domestic cup competitions as they reached the semi finals of both the FA Cup and league cup. They stumbled out of the last four of the league cup, suffering a 3-0 defeat against fellow division one counterparts, Tranmere Rovers. They came agonisingly close to reaching the final of the FA Cup as they forced Aston Villa to a penalty shoot out in a semi final encounter played at Wembley Stadium. Bolton’s new Icelandic signing, Eidur Gudjohnsen was in prolific form in front of goal, scoring 21 times during the 99-2000 campaign.
With Sam Allardyce in charge at the club, Bolton found their way to the top three of the first division during the 2000 – 2001 season. They finished off the campaign in an impressive third place and won the play off final to gain promotion back in to the premier league. Their new signing from Walsall, Michael Ricketts, scored 24 goals during the campaign which helped the Trotters discover their touch.
The start of the 2001- 02 season saw the arrival of former AC Milan player, Bruno N’Gotty, at the club. Allardyce took the club to new heights as he helped Bolton to a comfortable survival in their first season back in the top flight as they finished the campaign off in 16th place.

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