 On 2 April 2012, he was appointed as new head coach of Gubbio in the Italian Serie B league until the end of the season, thus becoming the fourth manager of the season for the small relegation-threatened Umbrian club (after Fabio Pecchia, Luigi Simoni and Marco Alessandrini).On 31 May 2018, Apolloni was appointed as the manager of Modena.It lasted until 10 January 2019, where he was fired.