He ended his playing career with Austrian club Red Bull Salzburg, where he then took the non-playing role of the reserve team coach and eventually became assistant manager under team manager Ricardo Moniz. In January 2013, Kovač took over the Croatia national under-21 team and in October 2013 he took over the Croatia senior team following the dismissal of Igor Štimac. Kovač managed Croatia at the 2014 FIFA World Cup, then became head coach of Eintracht Frankfurt in 2016, winning the 2018 DFB-Pokal Final with the club. At Bayern, Kovač won the domestic double in 2019 after a strong ending to the season, but lost his job later in that same autumn. In the summer of 2020, Kovač was appointed manager of Monaco.