 The following season, Markarian led them to the quarter finals of the UEFA Cup but lost to Jose Mourinho's FC Porto.In 2005, the Iraklis Thessaloniki Greek team hired him to help improve their first division standings.After coaching in Greece since 2002, Markarian returned to Paraguay to coach Libertad from 2005 to 2007, winning Paraguayan League titles in 2006 and 2007.