| 2. Round | 28/07/2012 | Preußen Münster | - | Chemnitzer FC | 1:0 | ||||
| 4. Round | 08/08/2012 | Preußen Münster | - | Hansa Rostock | 5:2 |  |
|||
| 5. Round | 11/08/2012 | SV Wehen Wiesbaden | - | Preußen Münster | 2:2 | |
|||
| 6. Round | 25/08/2012 | Preußen Münster | - | 1. FC Heidenheim 1846 | 1:1 |  |
|||
| 7. Round | 29/08/2012 | Hallescher FC | - | Preußen Münster | 0:2 | ||||
| 8. Round | 01/09/2012 | Preußen Münster | - | VfB Stuttgart II | 0:0 | |
|||
| 9. Round | 15/09/2012 | VfL Osnabrück | - | Preußen Münster | 0:2 | ||||
| 31. Round | 30/03/2013 | Borussia Dortmund II | - | Preußen Münster | 0:0 | ||||
| 32. Round | 06/04/2013 | Preußen Münster | - | 1. FC Saarbrücken | 3:3 | ||||
| 33. Round | 13/04/2013 | Kickers Offenbach | - | Preußen Münster | 0:1 | |
|||
| 27. Round | 16/04/2013 | VfB Stuttgart II | - | Preußen Münster | 0:1 | ||||
| 34. Round | 20/04/2013 | Preußen Münster | - | Karlsruher SC | 2:1 | |
|||
| 36. Round | 04/05/2013 | Preußen Münster | - | Stuttgarter Kickers | 0:1 | ||||
| 37. Round | 11/05/2013 | SpVgg Unterhaching | - | Preußen Münster | 3:0 | |
Germany