| 1. Round | 18/09/1999 | Iraklis Saloniki | - | Apollon Smyrnis | 1:0 | ||||
| 2. Round | 24/09/1999 | Apollon Smyrnis | - | Paniliakos Pyrgos | 0:0 |  |
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| 3. Round | 02/10/1999 | Apollon Smyrnis | - | Olympiakos Piraeus | 0:1 | |
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| 4. Round | 16/10/1999 | Ionikos Nikea | - | Apollon Smyrnis | 1:0 | ||||
| 5. Round | 23/10/1999 | Apollon Smyrnis | - | Aris Saloniki | 3:3 | ||||
| 6. Round | 31/10/1999 | OFI Heraklion | - | Apollon Smyrnis | 1:0 | ||||
| 7. Round | 06/11/1999 | Apollon Smyrnis | - | Skoda Xanthi | 0:0 | ||||
| 8. Round | 20/11/1999 | Panachaiki GE | - | Apollon Smyrnis | 1:2 | ||||
| 9. Round | 27/11/1999 | Apollon Smyrnis | - | AO Proodeftiki | 0:2 |
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