| 1. Round | 30/07/2016 | 1. FSV Mainz 05 II | - | FSV Zwickau | 2:2 | ||||
| 2. Round | 06/08/2016 | SC Paderborn 07 | - | 1. FSV Mainz 05 II | 3:1 | ||||
| 3. Round | 10/08/2016 | 1. FSV Mainz 05 II | - | VfL Osnabrück | 2:2 |  |
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| 4. Round | 13/08/2016 | MSV Duisburg | - | 1. FSV Mainz 05 II | 4:0 | ||||
| 5. Round | 27/08/2016 | Preußen Münster | - | 1. FSV Mainz 05 II | 1:0 | ||||
| 6. Round | 10/09/2016 | 1. FSV Mainz 05 II | - | 1. FC Magdeburg | 1:0 | ||||
| 7. Round | 17/09/2016 | Werder Bremen II | - | 1. FSV Mainz 05 II | 2:1 | ||||
| 8. Round | 21/09/2016 | 1. FSV Mainz 05 II | - | SV Wehen Wiesbaden | 1:2 | ||||
| 9. Round | 24/09/2016 | Holstein Kiel | - | 1. FSV Mainz 05 II | 3:0 | ||||
| 10. Round | 02/10/2016 | 1. FSV Mainz 05 II | - | Rot-Weiß Erfurt | 1:1 | ||||
| 11. Round | 16/10/2016 | Chemnitzer FC | - | 1. FSV Mainz 05 II | 4:1 |
Germany