In 1998, after a very poor campaign, ending in 10th of 12 teams, the club was relegated to the Campeonato Baiano Second Division. In 1999, Fluminense de Feira competed in the Campeonato Baiano Second Division, ending the competition as runner-up, after a 1–1 home match draw, and a 0–0 away match draw against Colo-Colo of Ilhéus. The team gained promotion to the following year's Campeonato Baiano first division.