[4] After finishing his playing career Kostenoglou joined the coaching staff at AEK Athens Academy.

AEK Athens was the best team that season, clinched first position in the league, but lost the championship due to legal action.

On 6 October 2011, he returned to AEK Athens for a second spell as manager, replacing Manolo Jiménez.

[6] while in July of the same year he was hired by Apollon Smyrnis in the second division,[7] from which he left in December.

[8] On 12 February 2015 he assumed the duties of assistant to the also newly hired Sergio Markarián in the Greece.