His coaching career started in Sochaux-Montbéliard where was an assistant and also a coach of the reserve squad. His first job as a head coach was at the Istres. He guided the club to its biggest success - entering the French Ligue 1 in 2004, which secured him a best Ligue 2 manager of the year award. On 16 July 2005, Baždarević took over Tunisian side Étoile Sportive du Sahel. He reached the 2005African Champions League final with the club. Baždarević was fired by Etoile on 12 April 2006, after a 1–0 home defeat to USM Monastir in their final league cost them the Tunisian League.
Baždarević was employed as a head coach of QatariAl-Wakra in 2006. In December 2006, he was a short list candidate for the Bosnia-Herzegovina national team coaching spot, but the job went to Fuad Muzurović instead.
Since December 2007, he has been managing French side Grenoble Foot 38 where he arrived on recommendation of his mentor Ivica Osim who knew Grenoble's Japanese owners from working with them in J-League with JEF United. At the end of 2007–08, led by Bazdarevic, Grenoble gained promotion to the French top league. In September 2010, he left Grenoble.
On 10 June 2011, Baždarević was named as manager of the Sochaux for which he played professional football. He was sacked on 6 March 2012, due to poor results.