Additions
| from | Name | Pos | Team | Team | ||
|---|---|---|---|---|---|---|
| 01/2009 |  | Armando Alonso | MF |  | Deportivo Saprissa | Saprissa |
| 01/2009 |  | Stefano Napoleoni | MF |  | Widzew Łódź | Widzew Łódź |
| 01/2009 |  | Piotr Piechniak | MF |  | Polonia Warszawa | Polonia Warszaw |
| 01/2009 |  | Toni Lehtinen | FW |  | Haka Valkeakoski | Haka |
| 07/2008 |  | Dimitrios Kyriakidis | GK |  | PAOK Saloniki | PAOK |
| 07/2008 | | Alexandros Paschalakis | GK | |||
| 07/2008 | | Kyriakos Stratilatis | GK |  | Aris Saloniki | Aris Saloniki |
| 07/2008 |  | Borislav Georgiev | DF | |||
| 07/2008 | | Mihalis Kapsis | DF | |||
| 07/2008 | | Georgios Koltzos | DF |  | Veria FC | Veria FC |
| 07/2008 |  | Fernando Machado | DF |  | Asteras Tripolis | Asteras |
| 07/2008 | | Theodoros Tripotseris | DF |  | Anorthosis Famagusta | Anorthosis |
| 07/2008 | | Michail Tzorbatzakis | DF |  | GS Kallithea | Kallithea |
| 07/2008 | | Georgios Katsikogiannis | MF |  | Olympiacos FC | Olympiacos FC |
| 07/2008 | | Kostas Kiassos | MF | |||
| 07/2008 |  | Alban Bushi | FW |  | Apollon Kalamarias | Ap. Kalamarias |
| 07/2008 | | Stelios Vasiliou | FW | |||
| 07/2008 |  | Moca Vukotić | MA |
Departures
| from | Name | Pos | Team | Team | ||
|---|---|---|---|---|---|---|
| 01/2009 | | Anastasios Pastos | DF |  | Pierikos Katerini | Pierikos Katerini |
| 07/2008 | | Giannis Firinidis | GK |  | Anagennisi Arta | Anagennisi Arta |
| 07/2008 |  | Anderson do Ó | DF |  | Vitória Setúbal | Vitória FC |
| 07/2008 | | Dimitrios Diamantis | MF |  | Ethnikos Asteras | Ethnikos Asteras |
| 07/2008 |  | Goran Popov | MF |  | Sc Heerenveen | Heerenveen |
| 07/2008 | | Ivan Rusev | MF |  | Diagoras FC | Diagoras FC |
| 07/2008 |  | Sebastian Schindzielorz | MF |  | VfL Wolfsburg II | Wolfsburg II |
| 07/2008 |  | Eli Kroupi | FW |  | Nîmes Olympique | Nîmes |
| 07/2008 |  | José Reyes | FW | | Ethnikos Asteras | Ethnikos Asteras |