on 29 january 2009, close to the january transfer window deadline, he signed 1 and a half year contract with croatian champions dinamo zagreb. the club previously tried to sign him in the summer of 2007, but failed to meet his demands. borussia dortmund were compensated with €450,000. in his debut season kovač made 12 appearances in the league and two more in croatian cup. he started the 2009–10 season with a foot injury and missed all of dinamo's matches in july and august, but returned to action at the start of the september. kovač finished the season with a total of 22 appearances for dinamo in all competitions, before it was officially announced on 1 june 2010 that he retired from active football.