In March 2017, Slišković again took the manager position at Zrinjski Mostar for the third time in his career, eventually ledaing the team to win the Bosnian Premier League in the 2016–17 season. In the 2017–18 season, he won his second league title in a row with Zrinjski. After winning two league trophies, Slišković left Zrinjski in June 2018. However, after the sacking of new manager Ante Miše, the club asked Slišković to return, which he agreed to on 13 August 2018. After the end of the 2018–19 Bosnian Premier League season, it was announced on 7 June 2019 that Slišković did not come to an agreement with the board of directors of Zrinjski on a contract extension and that he was leaving the club.