| 2. Round | 20/08/1999 | SpVgg Greuther Fürth | - | 1. FC Köln | 0:0 | ||||
| 3. Round | 27/08/1999 | 1. FC Köln | - | Stuttgarter Kickers | 4:1 | ||||
| 17. Round | 18/12/1999 | 1. FC Köln | - | Energie Cottbus | 4:1 | ||||
| 18. Round | 13/02/2000 | Rot-Weiß Oberhausen | - | 1. FC Köln | 1:0 | ||||
| 20. Round | 27/02/2000 | Stuttgarter Kickers | - | 1. FC Köln | 1:2 | ||||
| 27. Round | 16/04/2000 | 1. FC Köln | - | 1. FSV Mainz 05 | 1:0 | ||||
| 28. Round | 20/04/2000 | 1. FC Nürnberg | - | 1. FC Köln | 1:1 | ||||
| 31. Round | 14/05/2000 | 1. FC Köln | - | Karlsruher SC | 1:2 | ||||
| 32. Round | 18/05/2000 | Alemannia Aachen | - | 1. FC Köln | 1:2 |
Slovenia