Bundesliga. In the next round Preußen was defeated again by FC Augsburg. 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).
In the following seasons the team finished significantly better and even had chances to get promoted again to 2. Bundesliga. In season 2012-13 they almost succeeded and ended in fourth place.
After changing the coach from Horst Steffen to the former SCP-player Benno Möhlmann several high ranking positions in the club were also manned with new personalities. To serve as chairman Preußen Münster could win over Christoph Strässer, a former politician of the German Bundestag. Among others, the board of directors now contains Walther Seinsch who is well known in German football for his work with then fourth tier club FC Augsburg.
They were finally promoted to 3. Liga after finishing as champions of the West Group of the Regionalliga in the 2010-11 season. The manager of that time was Marc Fascher. Preußen were defeated by another Bundesliga team in the German cup, VfL Wolfsburg (1-2). The first season 2011-12 in the third tier of German football after five years ended with a 12th place.
- The club made only a cameo appearance in the Bundesliga, being relegated after a next-to-last 15th-place finish.
- V. which serves as a voice for supporters to club management.
- Due to the club’s promotion from Regionalliga West to 3.
- The opponent was VfL Bochum which competed in Bundesliga at that time.
In that season the team was also able to defeat the Bundesliga team Werder Bremen in the first round of the DFB-Pokal, 4-2 after extra time. In the second round the club lost against FC Augsburg. In season 2013-14 they ended in sixth place. Again the club managed to win against a team from a higher league in the DFB-Pokal, FC St. Pauli from 2.
In the 2014-15 season, the club had a promising start, and was during winter even at the top of the league. Unfortunately the team was not able to keep up the good results and finished 8th. The season 2015-16 also started with good results, but again the team lost ground in the long turn and finished ninth. During the season the club switched managers, from Ralf Loose to Horst Steffen. The following season brought up big changes in the club administration.
During its years in fourth tier of the German league system, the average crowd never exceeded 4,500 fans, with the exception of the 2010-11 season, during which the club was promoted, with an average attendance of 5,628. In the following years the average crowd grew from 7,025 people in 2011-12 season to 8,986 people in season 2012-13. In season 2013-14 there was a decrease to 7,958 people.