| 1. Round | 17/08/2008 | KRC Genk | - | Germinal Beerschot | 1:1 | ||||
| 2. Round | 23/08/2008 | Germinal Beerschot | - | FCV Dender EH | 1:1 | ||||
| 4. Round | 13/09/2008 | Germinal Beerschot | - | KSV Roeselare | 3:0 | ||||
| 5. Round | 20/09/2008 | Cercle Brugge | - | Germinal Beerschot | 1:0 |  |
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| 7. Round | 04/10/2008 | KV Kortrijk | - | Germinal Beerschot | 0:0 | ||||
| 8. Round | 18/10/2008 | Germinal Beerschot | - | Sporting Charleroi | 1:2 | ||||
| 9. Round | 25/10/2008 | RAEC Mons | - | Germinal Beerschot | 0:0 | ||||
| 12. Round | 15/11/2008 | SV Zulte Waregem | - | Germinal Beerschot | 2:2 | ||||
| 13. Round | 22/11/2008 | Germinal Beerschot | - | Sporting Lokeren | 0:2 | ||||
| 17. Round | 20/12/2008 | Germinal Beerschot | - | AFC Tubize | 2:0 | ||||
| 28. Round | 05/04/2009 | Standard Liège | - | Germinal Beerschot | 3:1 | ||||
| 29. Round | 11/04/2009 | Germinal Beerschot | - | SV Zulte Waregem | 1:2 | ||||
| 30. Round | 18/04/2009 | Sporting Lokeren | - | Germinal Beerschot | 1:0 |  |
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| 31. Round | 24/04/2009 | Germinal Beerschot | - | Club Brugge KV | 2:0 | ||||
| 33. Round | 08/05/2009 | Germinal Beerschot | - | KV Mechelen | 3:1 | |
Belgium