On 14 December, he took part in a friendly game against the Spanish club Barcelona playing 14 minutes before suffering a foot injury.

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[4] In the 2005–06 season, he played a total of four matches in the championship[5] 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.

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.

[8] 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.

Replacing defender Franck Karremana, Manucharyan came off the bench in the 58th minute while Haarlem eventually lost 1–6 at home.

[18] A few days later, on 3 February, Edgar went on loan to AGOVV Apeldoorn, coached by former Ajax player John van den Brom.

[19] Manucharyan's first game for the club was marked by a goal, contributing to his team's 0–1 win in the away league match against FC Volendam.

[24] He made his debut in the second leg of the 2010–11 Champions League second qualifying round tie with Partizan Belgrade.

After the end of his contract, Manucharyan became a free agent and with Ukrainian club FC Karpaty Lviv showing interest in signing him.