In July 2010, Zekić was appointed manager of Zagreb-based local football club Maksimir, which he managed until 2013. One year later he moved to Moldova, where he managed Sheriff-2 Tiraspol in 2014, after which he became Sheriff Tiraspol manager. He won the double with Sheriff in the 2014–15 season, winning the Divizia Naţională and the national cup.
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 drew Santa Coloma, Luzern and PSV Eindhoven. 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. On 29 March 2019, following a string of poor results in the league, Zekić parted ways with Osijek.[2]
On 30 April 2019, Zekić came back to manage Sheriff.[3] He managed to lead the side to another league and cup triumph, before leaving the club in October 2020.[4]