De Zerbi took his first coaching role in November 2013 at Serie D amateurs Darfo Boario.
In July 2014 he accepted an offer to become new head coach of his former club Foggia in the Lega Pro league, with whom he won a Coppa Italia Lega Pro in 2016 and narrowly missed promotion after a 5-3 aggregate loss to Pisa in the playoff finals.