In 2006, the club was relegated to the Oberliga Westfalen, now a fourth tier circuit. Management subsequently invested significant financial resources into a high-profile team of experienced second- and third-tier players in pursuit of immediate re-promotion. The attempt ended in failure and the club re-built itself with young players in place of expensive veterans and also put in place a young and relatively unknown coach, Roger Schmidt. The re-worked side finished in first place in the 2007–08 season, and so qualified for the new Regionalliga West which replaced the Oberliga in the league system. They ended the season in fourth place in the Regionalliga in 2008–09, and in sixth in 2009–10. For season 2008–09 the club qualified for the DFB-Pokal the first time since season 1997–98 (where they were defeated by 1.FSV Mainz 05). The opponent was VfL Bochum which competed in Bundesliga at that time. After a penalty shootout Preußen lost 5–6. In the following year the Eagles were defeated in the extra time against another first tier team, Hertha BSC. The match ended 1–3.