In the 2006–07 season, Manucharyan rarely got into the first team squad and was frequently injured. He mostly played for the youth team, Jong Ajax. On 2 November 2006, Manucharyan scored his first official goal for Ajax in a 3–0 win over Austrian club FK Austria Wien during the 2006–07 UEFA Cup season. Having come on as a substitute in the 57th minute, he scored 8 minutes later. On 22 July 2006, Manucharyan took part in a friendly match against English club Arsenal F.C., which was held at the new Emirates Stadium. The match was the farewell game for Dennis Bergkamp, former player of Ajax and Arsenal. Manucharyan made an assist to Klaas-Jan Huntelaar, who scored the first ever goal at the new Emirates Stadium. In early March 2007, he extended his contract until 2011, and in May he won his second KNVB Cup.