| 1. Round | 11/08/1999 | 1. FC Magdeburg | - | BFC Dynamo | 1:1 | ||||
| 2. Round | 14/08/1999 | Dresdner SC | - | 1. FC Magdeburg | 1:1 | ||||
| 3. Round | 20/08/1999 | 1. FC Magdeburg | - | VfB Leipzig | 0:1 |  |
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| 4. Round | 24/08/1999 | TeBe Berlin II | - | 1. FC Magdeburg | 1:3 | ||||
| 5. Round | 29/08/1999 | SV Babelsberg 03 | - | 1. FC Magdeburg | 2:3 | ||||
| 6. Round | 07/09/1999 | 1. FC Magdeburg | - | FSV Zwickau | 2:2 | ||||
| 7. Round | 11/09/1999 | Rot-Weiß Erfurt | - | 1. FC Magdeburg | 1:0 | |
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| 9. Round | 25/09/1999 | VfL Halle 96 | - | 1. FC Magdeburg | 2:2 | ||||
| 10. Round | 01/10/1999 | 1. FC Magdeburg | - | Dynamo Dresden | 1:2 | |
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| 18. Round | 05/02/2000 | BFC Dynamo | - | 1. FC Magdeburg | 0:2 | |
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| 20. Round | 18/02/2000 | VfB Leipzig | - | 1. FC Magdeburg | 1:0 | ||||
| 21. Round | 27/02/2000 | 1. FC Magdeburg | - | TeBe Berlin II | 6:1 | |
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| 22. Round | 05/03/2000 | 1. FC Magdeburg | - | SV Babelsberg 03 | 1:4 | ||||
| 23. Round | 11/03/2000 | FSV Zwickau | - | 1. FC Magdeburg | 0:3 | |
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| 25. Round | 25/03/2000 | Hertha BSC II | - | 1. FC Magdeburg | 0:2 dec. | ||||
| 26. Round | 02/04/2000 | 1. FC Magdeburg | - | VfL Halle 96 | 1:1 |
Poland