In the 3rd round of the 2012–13 Czech Cup on 26 September 2012 in a match against Chomutov, Malakyan came in when the score was a losing 1:2 and sharpened the game, gave the assists, and Victoria won 3–2.

On 8 November, for his debut in the UEFA Europa League against Hapoel Tel Aviv, Malakyan came out on the field for 46 minutes.

Becoming team captain and having good performances in UEFA Europa League qualifying playoffs, he was then bought by Ukrainian Stal Kamianske alongside his younger brother, Gor.

Since signing for the Ukrainian Premier League side in 2016, Edgar became a regular starter, key squad member and team captain as well.

[5] Malakyan debuted internationally on 12 August 2009 as part of the Armenia national football team in a friendly match against Moldova.