| 5. Round | 21/09/2008 | Hamburger SV II | - | 1. FC Magdeburg | 0:1 | ||||
| 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 | ||||
| 9. Round | 24/10/2008 | Sachsen Leipzig | - | 1. FC Magdeburg | 0:1 |  |
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| 10. Round | 29/10/2008 | 1. FC Magdeburg | - | VfB Lübeck | 3:0 | ||||
| 11. Round | 02/11/2008 | SV Wilhelmshaven | - | 1. FC Magdeburg | 2:2 |  |
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| 12. Round | 09/11/2008 | 1. FC Magdeburg | - | Hansa Rostock II | 2:1 | ||||
| 13. Round | 14/11/2008 | 1. FC Magdeburg | - | Energie Cottbus II | 3:1 | ||||
| 15. Round | 29/11/2008 | 1. FC Magdeburg | - | Türkiyemspor Berlin | 2:0 | ||||
| 14. Round | 03/12/2008 | Altona 93 | - | 1. FC Magdeburg | 0:0 | ||||
| 16. Round | 07/12/2008 | FC Oberneuland | - | 1. FC Magdeburg | 1:2 | |
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| 17. Round | 14/12/2008 | 1. FC Magdeburg | - | Chemnitzer FC | 4:1 | ||||
| 18. Round | 19/12/2008 | 1. FC Magdeburg | - | Hannover 96 II | 2:1 | ||||
| 19. Round | 21/02/2009 | Holstein Kiel | - | 1. FC Magdeburg | 1:1 | ||||
| 20. Round | 28/02/2009 | 1. FC Magdeburg | - | SV Babelsberg 03 | 1:1 | |
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| 21. Round | 08/03/2009 | Hallescher FC | - | 1. FC Magdeburg | 1:0 |
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