The 2008–09 season did not start well for Seitaridis, as he lost his place in the first team to new signings Tomáš Ujfaluši and John Heitinga, and his heavy contract meant that Atlético was looking to sell him. Despite that, Seitaridis was a starter in Atlético's opening game, in a 4–0 victory over Málaga CF, and went on to make 14 league appearances that season. On 29 April 2009 however, him and teammate Maniche were suspended by Atlético's president Enrique Cerezo because they failed to appear in an Atlético home match against Sporting Gijón despite not being included in the 18-man squad. Two weeks later on 13 May 2009, it was announced that Seitaridis was released by Atlético a year before his contract was to expire, with a statement on the club's official website reading "Seitaridis is therefore free to negotiate with other clubs who may be interested in signing him".