In early December 2004, Manucharyan joined Ajax Amsterdam. On 14 December, he took part in a friendly game against the Spanish club Barcelona playing 14 minutes before suffering a foot injury. As was later revealed in a medical examination, Manucharyan had broken the metatarsal bones in his right leg. The same day the Football Federation of Armenia named Manucharyan best player of Armenia in 2004 in a survey conducted among journalists. After the injury, Ajax did not immediately sign a contract with Manucharyan but in July 2005, he joined on a three-year contract with Ajax paying Pyunik a $100,000 fee.