| Year | Division | Position | Points | Goal
difference | Top goalscorer(s) | Cup | Europe |
| 1991–92 | NOFV-Oberliga Mitte (III) | 1st | 69:7 | +77 |  Matthias Zimmerling 20 | | |
| 1992–93 | NOFV-Oberliga Mitte (III) | 1st | 54:10 | +79 |  Jacek Mencel 24 | | |
| 1993–94 | NOFV-Oberliga Mitte (III) | 1st | 54:6 | +96 |  Goran Markov 21 | | |
| 1994–95 | Regionalliga Nordost (III) | 3rd | 47:21 | +39 | Goran Markov 20 | R64 | |
| 1995–96 | Regionalliga Nordost (III) | 2nd | 72 | +49 |  Sergej Barbarez 17 | | |
| 1996–97 | Regionalliga Nordost (III) | 5th | 62 | +14 | Norman Struck 10 | | |
| 1997–98 | Regionalliga Nordost (III) | 6th | 54 | +10 | Nico Patschinski 9 | | |
| 1998–99 | Regionalliga Nordost (III) | 6th | 57 | +30 | Steffen Menze 14 | | |
| 1999–2000 | Regionalliga Nordost (III) | 1st | 77 | +30 | Steffen Menze 13 | | |
| 2000–01 | Regionalliga Nord (III) | 1st  | 73 | +39 |  Daniel Teixeira 18 | RU | |
| 2001–02 | 2. Bundesliga (II) | 6th | 56 | +20 |  Sreto Ristić 14,  Kostadin Vidolov 10,  Harun Isa 9,  Cristian Fiél 7,
Petar Divić 7, Steffen Menze 6 | R16 | UC R64 |
| 2002–03 | 2. Bundesliga (II) | 9th | 45 | −12 | Steffen Baumgart 9, Kostadin Vidolov 6,  Salif Keita 5, Sreto Ristić 5 | R32 | |
| 2003–04 | 2. Bundesliga (II) | 17th  | 33 | −10 | Steffen Baumgart 13, Salif Keita 8, Thomas Sobotzik 7 | R32 | |
| 2004–05 | Regionalliga Nord (III) | 19th | 27 | −18 |  Ryan Coiner 12 | R64 | |
| 2005–06 | NOFV-Oberliga Nord (IV) | 1st | 69 | +51 | Daniel Teixeira 24 | | |
| 2006–07 | Regionalliga Nord (III) | 12th | 48 | +6 |  Karim Benyamina 11 | | |
| 2007–08 | Regionalliga Nord (III) | 4th | 60 | +18 | Nico Patschinski 13 | R64 | |
| 2008–09 | 3. Liga (III) | 1st | 78 | +36 | Karim Benyamina 16 | | |
| 2009–10 | 2. Bundesliga (II) | 12th | 44 | −3 | Torsten Mattuschka 10,  John Jairo Mosquera 7, Karim Benyamina 6,
Hüzeyfe Doğan 5, Kenan Şahin 5 | R64 | |
| 2010–11 | 2. Bundesliga (II) | 11th | 42 | −6 | John Jairo Mosquera 8, Karim Benyamina 7, Torsten Mattuschka 5 | R64 | |
| 2011–12 | 2. Bundesliga (II) | 7th | 48 | −3 | Simon Terodde 8, Silvio 8, Chinedu Ede 7, Christopher Quiring 6,
John Jairo Mosquera 6, Torsten Mattuschka 5 | R64 | |
| 2012–13 | 2. Bundesliga (II) | 7th | 49 | +1 | Simon Terodde 10, Torsten Mattuschka 10,  Adam Nemec 9 | R32 | |
| 2013–14 | 2. Bundesliga (II) | 9th | 44 | +1 | Torsten Mattuschka 12, Sören Brandy 11, Simon Terodde 5, Adam Nemec 5 | R16 | |
| 2014–15 | 2. Bundesliga (II) | 7th | 47 | -5 | Sebastian Polter 14,  Damir Kreilach 7 | R64 | |
| 2015–16 | 2. Bundesliga (II) | 6th | 49 | +6 | Bobby Wood 17, Damir Kreilach 12, Benjamin Kessel 6 | R64 | |
| 2016–17 | 2. Bundesliga (II) | 4th | 60 | +12 | Damir Kreilach 9, Steven Skrzybski 8, Sebastian Polter 7, Collin Quaner 7,  Philipp Hosiner 6 | R32 | |
| 2017–18 | 2. Bundesliga (II) | 8th | 47 | +8 | Steven Skrzybski 14, Sebastian Polter 12 | R32 | |
| 2018–19 | 2. Bundesliga (II) | 3rd | 57 | +21 |  Sebastian Andersson 14, Sebastian Polter 9, Grischa Prömel 7, Akaki Gogia 6, Joshua Mees 6 | R32 | |
| 2019–20 | Bundesliga (I) | 11th | 41 | −17 | Sebastian Andersson 12, Marius Bülter 7,  Marcus Ingvartsen 5 | QF | |
| 2020–21 | Bundesliga (I) | 7th | 50 | +7 | Max Kruse 11,  Joel Pohjanpalo 6, Marvin Friedrich 5, Robert Andrich 5,  Taiwo Awoniyi 5 | R32 | |
| 2021–22 | Bundesliga (I) | 5th | 57 | +6 | Taiwo Awoniyi 15, Grischa Prömel 8, Max Kruse 5 | SF | UECL GS |
| 2022–23 | Bundesliga (I) | 4th | 62 | +13 |  Sheraldo Becker 11, Kevin Behrens 8,  Danilho Doekhi 5, Janik Haberer 5 | QF | UEL R16 |
