| 1. Round | 20/08/2006 | Ergotelis | - | Ionikos Nikea | 1:1 | ||||
| 2. Round | 26/08/2006 | Panathinaikos | - | Ionikos Nikea | 0:2 | ||||
| 3. Round | 10/09/2006 | Ionikos Nikea | - | Apollon Kalamarias | 1:0 | ||||
| 9. Round | 05/11/2006 | Skoda Xanthi | - | Ionikos Nikea | 2:0 |  |
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| 10. Round | 12/11/2006 | Ionikos Nikea | - | Panionios GSS | 1:1 | ||||
| 11. Round | 19/11/2006 | PAOK Saloniki | - | Ionikos Nikea | 3:0 | ||||
| 12. Round | 26/11/2006 | Ionikos Nikea | - | OFI Heraklion | 0:2 | ||||
| 13. Round | 02/12/2006 | AEK Athen | - | Ionikos Nikea | 2:0 | ||||
| 15. Round | 16/12/2006 | Olympiakos Piraeus | - | Ionikos Nikea | 3:0 | ||||
| 16. Round | 07/01/2007 | Ionikos Nikea | - | Ergotelis | 1:3 |
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