| 3. Round | 10/09/2016 | Hibernians FC | - | Mosta FC | 3:1 | ||||
| 4. Round | 17/09/2016 | Mosta FC | - | Gżira United | 2:1 | ||||
| 5. Round | 22/09/2016 | Birkirkara FC | - | Mosta FC | 2:0 | ||||
| 6. Round | 26/09/2016 | Mosta FC | - | St. Andrews FC | 1:0 | ||||
| 7. Round | 30/09/2016 | Mosta FC | - | Hamrun Spartans | 2:5 | ||||
| 9. Round | 22/10/2016 | Mosta FC | - | Floriana FC | 0:1 |  |
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| 10. Round | 30/10/2016 | Sliema Wanderers | - | Mosta FC | 1:1 | ||||
| 11. Round | 05/11/2016 | Mosta FC | - | Pembroke Athleta FC | 0:3 | ||||
| 15. Round | 10/12/2016 | Gżira United | - | Mosta FC | 3:0 | ||||
| 16. Round | 04/01/2017 | Mosta FC | - | Birkirkara FC | 0:2 | ||||
| 17. Round | 07/01/2017 | St. Andrews FC | - | Mosta FC | 1:1 | ||||
| 18. Round | 14/01/2017 | Mosta FC | - | Tarxien Rainbows | 0:2 |
Slovakia