After finishing his playing career, Muratović spent more than two years as head scout of Austrian Bundesliga club Sturm Graz from July 2017 to September 2019.

From May 2019 until December 2020, he worked as the sporting director of Bosnian Premier League club Tuzla City.

Muratović then had a short spell at Chemnitzer FC and then moved to Russian Premier League club Saturn Ramenskoye.

He made his debut for Bosnia and Herzegovina in a January 1999 friendly match away against Malta and has earned a total of 24 caps, scoring no goals.

On 29 May 2019, he was named new sporting director of Bosnian Premier League club Tuzla City.