He then worked as an assistant coach with the Greek clubs Near East, Aris Thessaloniki, and Sporting Athens.

He was an assistant coach with the Lithuanian League club, Žalgiris Kaunas, in the 2011–12 season for a few months, being fired by controversial owner Vladimir Romanov for poor preparation of the team during the pre-season.

He was then an assistant coach with the Russian VTB United League club, UNICS Kazan, in the 2013–14 season.

[2] On January 28, 2020, Kantzouris signed with Greek Basket League club Iraklis (his first official head coaching job), replacing Ioannis Kastritis.

On July 3, 2022, after two successful seasons with Kolossos Rodou, Kantzouris was named head coach of AEK Athens.