On 27 April 2009 Hearts announced that Karipidis had a pre-contract agreement with Omonia Nicosia which would see him join the Cypriot side on a three-year deal at the end of the season. He stated that although he had enjoyed his time in Scotland, the move was motivated by his desire to be closer to his home and relatives in Greece. His final appearance at Tynecastle came in a 3–0 victory over Dundee United which confirmed Hearts' place in the Europa League for the following season and third place in the SPL. He was replaced by Jason Thomson in the closing stages of the match and received a standing ovation from the Hearts fans.