| 7. Round | 28/08/2012 | 1. FC Heidenheim 1846 | - | Chemnitzer FC | 3:2 | ||||
| 8. Round | 02/09/2012 | SV Darmstadt 98 | - | 1. FC Heidenheim 1846 | 0:2 | ||||
| 9. Round | 16/09/2012 | 1. FC Heidenheim 1846 | - | Hansa Rostock | 1:2 | ||||
| 11. Round | 26/09/2012 | Wacker Burghausen | - | 1. FC Heidenheim 1846 | 4:1 | ||||
| 12. Round | 29/09/2012 | 1. FC Heidenheim 1846 | - | Hallescher FC | 3:1 | ||||
| 13. Round | 06/10/2012 | VfB Stuttgart II | - | 1. FC Heidenheim 1846 | 0:2 | ||||
| 15. Round | 27/10/2012 | Arminia Bielefeld | - | 1. FC Heidenheim 1846 | 1:0 | ||||
| 16. Round | 02/11/2012 | 1. FC Heidenheim 1846 | - | Alemannia Aachen | 1:1 | ||||
| 17. Round | 10/11/2012 | Borussia Dortmund II | - | 1. FC Heidenheim 1846 | 2:1 | ||||
| 24. Round | 02/02/2013 | SV Babelsberg 03 | - | 1. FC Heidenheim 1846 | 2:4 | ||||
| 30. Round | 16/03/2013 | 1. FC Heidenheim 1846 | - | Wacker Burghausen | 2:1 | ||||
| 32. Round | 06/04/2013 | 1. FC Heidenheim 1846 | - | VfB Stuttgart II | 1:0 | ||||
| 34. Round | 20/04/2013 | 1. FC Heidenheim 1846 | - | Arminia Bielefeld | 3:0 |  |
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| 36. Round | 04/05/2013 | 1. FC Heidenheim 1846 | - | Borussia Dortmund II | 2:2 |
Germany