| Group D | 01/12/2016 | Xanthi FC | - | AEL Kalloni | 3:1 | ||||
| Group D | 13/12/2016 | Agrotikos Asteras | - | Xanthi FC | 1:1 | ||||
| Round of 16 | 24/01/2017 | Xanthi FC | - | OFI Heraklion | 1:0 | ||||
| Round of 16 | 31/01/2017 | OFI Heraklion | - | Xanthi FC | 2:1 |  |
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| Quarter-finals | 09/02/2017 | Xanthi FC | - | PAOK Saloniki | 1:2 | |
Greece