Mombaerts began his coaching career with Paris Saint-Germain, taking charge between October 1987 and February 1988.[4] Mombaerts was manager of Guingamp during the 1989–90 season.[4] He then managed Cannes between January 1992 and December 1992,[4] and Toulouse from 2001 to 2006.[4] While with Toulouse he won the Ligue 2 championship in 2003.[5]
Mombaerts became manager at Le Havre in December 2012.[7] He resigned in December 2014.[8]
He was appointed as the head coach of Japanese club Yokohama F. Marinos in December 2014.[9]
Mombaerts stepped down as head coach of the Marinos at the succession of the 2017 Emperor's Cup, on 1 January 2018.[10][11]
Mombaerts was appointed manager of Melbourne City on 27 June 2019.[12] On 3 September 2020, he stood down from the coaching role at City to return to France, handing the coaching reins over to his assistant Patrick Kisnorbo.[13]