The 2008-09 season was the 95th season in Aris Thessaloniki F.C.'s existence. The club finished 6th in the Super League. Aris Thessaloniki was eliminated on penalties in the fifth round of Greek Football Cup by PAOK. On the UEFA Cup, the croatian Slaven Koprivnica eliminated Aris Thessaloniki in the Second qualifying round. Dušan Bajević removed from manager's position in July. Quique Hernández came after him. In January, Quique Hernández replaced by Iomar Mazinho and his assistant Donato Gama Aris Thessaloniki hired Giorgos Koltsidas as technical director after his retirement as player.