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 its 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 decline 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.
The highly popular Volkan Uluc returned as coach on 1 July 2012. Central players in the team were Christian Preiß, Nico Patschinski, Matthias Steinborn, Kevin Gutsche, Christof Köhne, Carsten Busch, Ibrahim Keser, Patrick Brendel and Tom Butzmann. BFC Dynamo was a top team in the league and finished the 2012–13 NOFV-Oberliga Nord in third place. BFC Dynamo then defeated SV Lichtenberg 47 1–0 in the final of the 2012–13 Berlin Cup. The club signed Senegalese striker Djibril N'Diaye for the 2013–14 season. N'Diaye would quickly become a crowd favorite and known by the name "Dieter". BFC Dynamo lost 0–2 against VfB Stuttgart in the first round of the 2013–14 DFB-Pokal. The team dominated the 2013–14 NOFV-Oberliga Nord. BFC Dynamo went through the entire league season undefeated. BFC Dynamo finished the 2013–14 NOFV-Oberliga Nord in first place and thus had finally won promotion to the Regionaliga Nordost after ten years in the NOFV-Oberliga Nord. BFC Dynamo returned to the Friedrich-Ludwig-Jahn-Sportpark in Prenzlauer Berg for the 2014–15 season. The 2014–14 Regionalliga Nordost also saw the return of BFC Dynamo to live television. Thomas Stratos became the new coach during the autumn of 2014. BFC Dynamo defeated SV Tasmania Berlin 2–1 in the final of the 2014–15 Berlin Cup. The club had thus won its fourth Berlin Cup title. BFC Dynamo finished the 2014–15 Regionliga Nordost in fifth place. The team was joined by Brazilian midfielder Thiago Rockenbach, midfielder Kai Pröger and striker Dennis Srbeny for the 2015–16 season. BFC Dynamo lost 0–2 to FSV Frankfurt in the first round of the 2015–16 DFB-Pokal. The club celebrated its 50th anniversary on 15 January 2016. BFC Dynamo finished the 2016–17 Regionalliga Nordost in a meager 15th place, but the team again reached the final of the Berlin Cup. BFC Dynamo eventually defeated FC Viktoria 1889 Berlin 3–1 in the final of the 2016–17 Berlin Cup.
BFC Dynamo recruited Azerbaijan national team player Rufat Dadashov for the 2017–18 season. The team drew FC Schalke 04 in the first round of the 2017–18 DFB-Pokal. BFC Dynamo lost 0–2 against FC Schalke 04 in front of 14,114 spectators at Friedrich-Ludwig-Jahn-Sportpark. Dadashov finished as top scorer in the 2017–18 Regionalliga Nordost with 25 goals. BFC Dynamo defeated Berliner SC 2–1 in the final of the 2017–18 Berlin Cup to win its second consecutive Berlin Cup title. BFC Dynamo faced 1. FC Köln in front of 14,357 at the Olympiastadion in the first round of the 2018–19 DFB-Pokal. The attendance number set a new record for BFC Dynamo since the fall of the Berlin Wall. Patrik Twardzik made it 1-0 for BFC Dynamo in the 19th minute, but 1. FC Köln eventually won the match 1–9.
Christian Benbennek became the new coach for the 2019–20 season. Both the 2019–20 Regionalliga Nordost and the 2020–21 Regionalliga Nordost would be cancelled due to the ongoing COVID-19 pandemic. BFC Dynamo defeated Berliner AK 07 2–1 in the final of the 2020–21 Berlin Cup. BFC Dynamo was joined by experienced centre-forward Christian Beck and goalkeeper Dmitri Stajila for the 2021–22 season. Key players in the team were Christian Beck, Dmitri Stajila, Chris Reher, Alexander Siebeck, Michael Blum, Andreas Pollasch, Joey Breitfeld, Darryl Geurts, Andor Bolyki, Niklas Brandt and Philip Schulz. The team had great success in the league. BFC Dynamo finished the 2021–22 Regionalliga Nordost in first place and finally won its first Regionalliga title. The team would face VfB Oldenburg from the Regionalliga Nord in the play-offs to 3. Liga. With the help of sponsors and supporters, the club managed to collect the guarantee of 900,000 Euros in cash that was required in order to obtain a license to the 3. Liga. BFC Dynamo eventually lost the play-offs on goal difference and had narrowly missed promotion to the 3. Liga
Consolidation in the NOFV-Oberliga and rise (2004–2014) Mario Weinkauf era (2004–2006) BFC Dynamo finished the 2003-04 Verbandsliga Berlin in first place and qualified for the NOFV-Oberliga Nord. Club President Mike Peters announced that he would not stand for re-election. Mario Weinkauf was then elected new president on 18 June 2004. Weinkauf was the regional manager of a telecommunications company. When he was 18, he moved from Rostock to Berlin to study. In 1996, he enrolled his son in the youth department of FC Berlin. As a parent, he eventually became involved with the club. Weinkauf played in the old men's team and had earlier been a youth trainer at the club. Weinkauf was one of the seven founding members who had recently set up the sponsor association for the youth department. His vision for BFC Dynamo was a club that was "managed seriously from a sporting and financial perspective". The club was in need of a new main sponsor and the company Infinity-Net Telekom GmbH became new shirt sponsor for the 2004–05 season.
The former professional player of BFC Dynamo Christian Backs became the new coach from 1 June 2004. The two strikers Danny Kukulies and Tomasz Suwary were central players on the squad. Other central players were Jörn Lenz, Nico Thomaschewski and Robert Rudwaleit. The team was also joined by forward Dennis Kutrieb from SV Lichtenberg 47 and midfielder Maurice Jacobsen from Reinickendorfer Füchse, who would be important to the team during the season. The match between SV Babelsberg 03 and BFC Dynamo in 2004-05 NOFV-Oberliga Nord at the Karl-Liebknecht-Stadion on 14 August 2004 ended with riots. Supporters of BFC Dynamo invaded the pitch after the final whistle and hostilities between the two sets of supporters continued outside the stadium. At the same time, the club management engaged in several activities to try to improve the club's image. The Federal Centre for Health Education (BZgA) was invited to present its campaign against alcohol at the Stadion im Sportforum before the match against FC Schönberg 95 on 4 September 2004. The Kita-Project now looked after about 300-700 children per month. The club had also created a special block in the main stand of the stadium with free admission for young people under 16 years. BFC Dynamo surpassed its goal for the first half of the 2004–05 season. The team had only lost the match against the first-placed reserve team of FC Hansa Rostock and stood in sixth place after the first half of the season. BFC Dynamo had about 1,000 spectators on average per match during the first half of the season.
Fightings broke out between supporters of BFC Dynamo and police during the match between Tennis Borussia Berlin and BFC Dynamo at the Mommsenstadion on 11 February 2005. The police had decided to intervene against away supporters after a fare had been lit in the guest block. Police officers were pelted with beer mugs and attacked by supporters of BFC Dynamo when they entered the guest block. The club management announced on 23 February 2005 that the club would not apply for a license for Regionalliga Nordost, despite the team being in third place in the league. The financial consolidation was not yet complete. President Weinkauf announced that only basic compensation could be paid to players. Victory bonuses were still open. Coach Christian Backs then chose to leave for Berliner AK 07 due to financial disagreements with the club. He signed a one-year contract with Berliner AK 07 for the coming season and was given a leave of absence by BFC Dynamo. Assistant coach Rajko Fijalek and goalkeeper coach Bodo Rudwaleit took over as coaches for the rest of the season. BFC Dynamo played a friendly match against the Turkey national under-21 football team at the Stadion im Sportforum on 18 May 2005. The friendly match was kicked off by the Turkish boxer Sinan Şamil Sam, nicknamed the "Bull of the Bosphorus". The team won the match 4–3, with two goals by Dennis Kutrieb. BFC Dynamo defeated FSV Optik Rathenow 3–0 in the final matchday of the league season. The finished 2004-05 NOFV-Oberliga Nord in sixth place. Kutrieb left for SC Rot-Weiß Oberhausen and Maurice Jacobsen for Berliner AK 07 after the season.