| 28. Round | 29/03/2009 | Stuttgarter Kickers | - | Bayern München II | 0:0 | ||||
| 29. Round | 01/04/2009 | Bayern München II | - | Fortuna Düsseldorf | 0:1 | ||||
| 30. Round | 04/04/2009 | SpVgg Unterhaching | - | Bayern München II | 2:1 | ||||
| 31. Round | 12/04/2009 | Bayern München II | - | SV Sandhausen | 2:1 | ||||
| 21. Round | 15/04/2009 | Bayern München II | - | Wuppertaler SV | 2:0 | ||||
| 32. Round | 19/04/2009 | Jahn Regensburg | - | Bayern München II | 1:2 | ||||
| 33. Round | 26/04/2009 | Bayern München II | - | Erzgebirge Aue | 2:3 | ||||
| 34. Round | 01/05/2009 | Rot-Weiß Erfurt | - | Bayern München II | 1:1 | ||||
| 35. Round | 09/05/2009 | Bayern München II | - | Kickers Emden | 4:0 | ||||
| 36. Round | 13/05/2009 | Bayern München II | - | Wacker Burghausen | 3:1 | ||||
| 37. Round | 16/05/2009 | VfB Stuttgart II | - | Bayern München II | 2:2 | ||||
| 38. Round | 23/05/2009 | Bayern München II | - | Kickers Offenbach | 1:1 |
Germany