On 1 September 2015, Zekić was appointed manager of hometown club Osijek in the Croatian Prva HNL, signing a three-year contract until June 2018.

[1] In the 2016–17 season, Osijek finished in fourth place, earning a spot in the 2017–18 UEFA Europa League first qualifying rounds.

Osijek beat PSV with 2–0 on aggregate (0–1, 1–0), being promoted to the play-off round, where the club lost to Austria Wien on away goals.

[8] In his first game in charge, Sarajevo beat Aktobe in the 2024–25 UEFA Conference League first qualifying round on 11 July 2024.

[10] On 4 August 2024, Zekić earned victory in his first match of the league season, as Sarajevo defeated Sloboda Tuzla 3–1 at home.