Additions
| from | Name | Pos | Team | Team | ||
|---|---|---|---|---|---|---|
| 01/2009 |  | Kostas Nebegleras | MF |  | Aris Saloniki | Aris Saloniki |
| 07/2008 | | Michalis Kyrgias | DF |  | Atromitos U19 | Atromitos U19 |
| 07/2008 |  | Carlos Massara | DF |  | Asteras Tripolis | Asteras |
| 07/2008 | | Athanasios Papageorgiou | DF |  | AS Rhodos | AS Rhodos |
| 07/2008 | | Apostolos Skondras | DF |  | Panegialios FC | Panegialios FC |
| 07/2008 |  | Eduardo Brito | MF |  | Apollon Kalamarias | Ap. Kalamarias |
| 07/2008 | | Lucas Favalli | MF | | Apollon Kalamarias | Ap. Kalamarias |
| 07/2008 | | Andreas Tatos | MF |  | AO Chaidari | AO Chaidari |
| 07/2008 |  | Dominique Wassi | FW |  | FC Schalke 04 II | Schalke II |
Departures
| from | Name | Pos | Team | Team | ||
|---|---|---|---|---|---|---|
| 02/2009 |  | Roberto Merino | MF |  | US Salernitana 1919 | Salernitana |
| 07/2008 | | Konstantinos Andriolas | GK |  | Panionios GSS | Panionios |
| 07/2008 |  | César Castro | DF |  | PAS Giannina | PAS Giannina |
| 07/2008 | | Dimitrios Geladaris | DF |  | Ergotelis | Ergotelis |
| 07/2008 | | Georgios Georgiou | DF |  | Anorthosis Famagusta | Anorthosis |
| 07/2008 | | Dimitrios Ioannou | DF |  | AO Kerkyra | AO Kerkyra |
| 07/2008 | | Angelos Zouboulakis | DF |  | Fostiras FC | Fostiras FC |
| 07/2008 | | Guillermo Hoyos | MF |  | Poseidon Neon Poron | Poseidon Neon Poron |
| 07/2008 | | Georgios Korakakis | MF |  | Diagoras FC | Diagoras FC |
| 07/2008 | | Lê | MF |  | CD Águila | Águila |
| 07/2008 | | Luciano | MF | | PAS Giannina | PAS Giannina |
| 07/2008 | | Giannis Skopelitis | MF | | Anorthosis Famagusta | Anorthosis |
| 07/2008 | | Cirio | FW |  | Orihuela CF | Orihuela CF |
| 07/2008 |  | Roberto Sánchez | FW |  | Hapoel Ramat Gan | Hapoel Ramat Ga |
| 07/2008 | | Athanasios Tsigas | FW |  | AE Lárissa | AE Lárissa |