Clement was hired by Bayern Munich in June 2016 as their assistant manager, again working alongside Ancelotti. He helped Bayern to win the 2016 DFL-Supercup, beating Borussia Dortmund 2–0. Whilst at the club, Clement and Ancelotti changed their usual coaching method of man marking to resemble the zonal marking employed by former Bayern manager Pep Guardiola. As of December 2016, Clement and Ancelotti only lost one match during their time in the Bundesliga.