| 4. Round | 13/09/2008 | 1. FC Magdeburg | - | Hallescher FC | 1:2 | ||||
| 5. Round | 21/09/2008 | Hamburger SV II | - | 1. FC Magdeburg | 0:1 |  |
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| 6. Round | 26/09/2008 | 1. FC Magdeburg | - | Hertha BSC II | 2:0 | ||||
| 7. Round | 04/10/2008 | VfL Wolfsburg II | - | 1. FC Magdeburg | 1:2 | ||||
| 8. Round | 18/10/2008 | 1. FC Magdeburg | - | VFC Plauen | 0:0 | ||||
| 12. Round | 09/11/2008 | 1. FC Magdeburg | - | Hansa Rostock II | 2:1 | ||||
| 18. Round | 19/12/2008 | 1. FC Magdeburg | - | Hannover 96 II | 2:1 | |
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| 20. Round | 28/02/2009 | 1. FC Magdeburg | - | SV Babelsberg 03 | 1:1 | ||||
| 23. Round | 22/03/2009 | Hertha BSC II | - | 1. FC Magdeburg | 1:0 | ||||
| 25. Round | 12/04/2009 | VFC Plauen | - | 1. FC Magdeburg | 3:4 | ||||
| 26. Round | 17/04/2009 | 1. FC Magdeburg | - | Sachsen Leipzig | 0:0 | ||||
| 28. Round | 03/05/2009 | 1. FC Magdeburg | - | SV Wilhelmshaven | 1:0 | ||||
| 29. Round | 08/05/2009 | Hansa Rostock II | - | 1. FC Magdeburg | 4:2 | ||||
| 30. Round | 16/05/2009 | Energie Cottbus II | - | 1. FC Magdeburg | 0:2 | ||||
| 31. Round | 20/05/2009 | 1. FC Magdeburg | - | Altona 93 | 4:1 | ||||
| 32. Round | 22/05/2009 | Türkiyemspor Berlin | - | 1. FC Magdeburg | 2:0 | ||||
| 34. Round | 07/06/2009 | Chemnitzer FC | - | 1. FC Magdeburg | 1:1 |
Germany