On 27 December 2012, Bonačić joined Mes Kerman as head coach for the second time but left the team at the end of the season after leading the club at the sixth place. On 1 July 2013, he was named as the head coach of Zob Ahan, signed a one-year contract with the club. On 16 December 2013, it was announced that Luka will leave Zob Ahan in January 2014 and will be succeeded by Mojtaba Taghavi. On 23 January 2014, Luka returns as manager of Mes Kerman with signing a contract until the end of the season. He led Mes Kerman to the Hazfi Cup final for the first time, however, his side lost the match 1–0 to Tractor Sazi. On 6 April, Mes Kerman relegated to the Azadegan League after a 0–0 draw with Saba Qom. He was given a one-year contract by the club to lead them in Azadegan League and promotion back Mes Kerman to the Iran Pro League at the end of the season. However, he was sacked on 11 November 2014 after poor results. On 21 November 2014, he was named as manager of Qatar Stars League side Al-Shahania.