| 1. Round | 22/08/2012 | FC Brussels | - | Royal Mouscron-Péruwelz | 0:0 | ||||
| 2. Round | 29/08/2012 | Royal Mouscron-Péruwelz | - | RBD Borinage | 3:1 | ||||
| 3. Round | 01/09/2012 | Royal Mouscron-Péruwelz | - | KAS Eupen | 1:0 | ||||
| 8. Round | 05/10/2012 | Royal Mouscron-Péruwelz | - | Sint-Truidense VV | 3:1 | ||||
| 9. Round | 13/10/2012 | KV Oostende | - | Royal Mouscron-Péruwelz | 1:1 |  |
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| 10. Round | 21/10/2012 | Royal Mouscron-Péruwelz | - | KSV Oudenaarde | 0:1 | ||||
| 11. Round | 27/10/2012 | R. White Star Woluwe FC | - | Royal Mouscron-Péruwelz | 2:1 | |
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| 23. Round | 02/02/2013 | KSV Roeselare | - | Royal Mouscron-Péruwelz | 0:3 | ||||
| 24. Round | 10/02/2013 | Royal Mouscron-Péruwelz | - | KVC Westerlo | 1:0 | ||||
| 26. Round | 22/02/2013 | Royal Mouscron-Péruwelz | - | KV Oostende | 2:0 | ||||
| 28. Round | 09/03/2013 | Royal Mouscron-Péruwelz | - | R. White Star Woluwe FC | 1:1 | ||||
| 29. Round | 16/03/2013 | Eendracht Aalst | - | Royal Mouscron-Péruwelz | 1:0 | |
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| 34. Round | 28/04/2013 | CS Visé | - | Royal Mouscron-Péruwelz | 1:3 |
France