BFC Dynamo finished the 2003–04 Verbandsliga Berlin in first place and won promotion back to the NOFV-Oberliga Nord. Mario Weinkauf was elected as the new club president on 18 June 2004. His vision was a club that was "managed seriously from a sporting and financial perspective". Former professional player Christian Backs became the new coach for the 2004–05 season. Rajko Fijalek served as assistant coach and former professional goalkeeper Bodo Rudwaleit as goalkeeping coach. Central players in the team were Robert Rudwaleit, Nico Thomaschewski, Dennis Kutrieb, Jörn Lenz and Danny Kukulies. BFC Dynamo finished is first season in the NOFV-Oberliga Nord, since returning from the insolvency crisis, in sixth place.
Former FC Vorwärts Berlin player Jürgen Piepenburg took over as new coach for the 2005–06 season. The 2005–06 NOFV-Oberliga Nord meant new meetings with arch-rival 1. FC Union Berlin. BFC Dynamo lost the first match against 1. FC Union Berlin 8–0 away at the Stadion an der Alten Försterei. Coach Piepenburg was dismissed after the match. BFC Dynamo celebrated 40 years on 16 January 2006. The club management worked to improve the club's reputation. BFC Dynamo got a new sponsor from Israel, and sponsor agreements with controversial sponsors were terminated. The index of terminated agreements included several companies with links to Hells Angels. The return match against 1. FC Union Berlin at the Stadion im Sportforum on 13 May 2006 was abandoned when supporters of BFC Dynamo invaded the pitch to attack the supporters of 1. FC Union Berlin.
The club was thrown into a new financial crisis after the riots in the match against 1. FC Union Berlin. The club's finances were saved by the sponsor Infinity-Net Telefon GmbH. The company's owner Peter Meyer became the club's new strongman. BFC Dynamo was a relegation candidate after the first half of the 2006–07 NOFV-Oberliga Nord. Turkish-born Volkan Uluc became the new coach on 9 March 2007. The team then began a slow rise in the league. A power struggle developed between president Weinkauf and main sponsor Meyer. Weinkauf was eventually dismissed at the annual meeting on 23 June 2007 and Meyer was elected chairman of the Economic Council. Veteran Jörn Lenz ended his playing career after the 2007–08 season. He had played a total of 374 matches for BFC Dynamo since 1988. Lenz continued in the club as team manager.
The team got off to a good start in the 2008–09 NOFV-Oberliga Nord. Norbert Uhlig became the new club president on 11 October 2008. BFC Dynamo eventually finished the 2008–09 NOFV-Oberliga Nord as runner-up. Christian Backs returned as coach for the 2009–10 season. The team reached the final of the 2009–10 Berlin Cup and finished the 2009–10 NOFV-Oberliga Nord in second place. Goalkeeper Nico Thomaschewski ended his playing career after the 2009–10 season. BFC Dynamo saw a descline in the league in the following season, but the team was again successful in the Berlin Cup. BFC Dynamo defeated SFC Stern 1900 in the final of the 2010–11 Berlin Cup and won its second Berlin Cup title. BFC Dynamo lost 0–2 to 1. FC Kaiserslautern in the first round of the 2011–12 DFB-Pokal in front of 10,104 spectators at the Friedrich-Ludwig-Jahn-Sportpark. The match ended with a scandal when 200-300 supporters of BFC Dynamo stormed the guest block after the final whistle.