Manucharyan scored his first goal for Ajax in an 18–0 pre-season win over a Dutch amateur side. Manucharyan made his Ajax and his Eredivisie debut on 18 September 2005 in a 4–2 defeat to AZ Alkmaar coming off the bench in the 84th minute in place of striker Ryan Babel In the 2005–06 season, he played a total of four matches in the championship and won the KNVB Cup. He also participated in the Amsterdam Tournament of 2006 coming on as a substitute against Inter Milan and featuring in the starting line-up against Manchester United. After the match, both Olympique Lyonnais and S.L. Benfica showed interest in the player. However, on 16 March 2007 his running contract until 2008 was extended until 30 June 2011.