 At the end of the year, the team went bankrupt and was placed in Eccellenza.In the 2004–05 season of Eccellenza Apulia, Brindisi placed second, qualifying for the national playoffs.The team won its two rounds in the playoffs, thus winning promotion to Serie D.

For the next 4 season, the team played in Serie D. In the 2008–09 season, Brindisi clinched first place in Girone H, thus gaining direct promotion to Lega Pro Seconda Divisione.