Božidar started his coaching career as an assistant coach at Greek clubs FC Akratitos (2004-05) and FC Kerkyra (2005-06) and helped the clubs win promotion from the second division. Between the years 2008 and 2010, he was assistant coach at Olympiacos and temporarily took over as head coach as well for a brief period. He won the SuperLeague Greece, the Greek Cup and the Greek Super Cup as assistant manager. In 2014, Bandović moved to Thailand to manage Buriram United and a couple of other Thai professional clubs over the next few years. He won the league twice with BUFC and was also named Thai Premier League (Thai League 1) coach of the year in 2018.
The UEFA Pro Licence holder joined Chennaiyin FC prior to the start of the 2021-22 ISL season. However, CFC’s performances have fallen off the cliff this season. They lie in eighth place having scored the least number of goals in the league. Bandović will be replaced by current assistant coach Syed Sabir Pasha who will take over as interim manager.