In September 2009, he left Salernitana by mutual consent in order to return to Messina, joining the giallorossi, now in Serie D, on a free transfer with the aim to guide them back into professionalism.

[7] After his retirement, Di Napoli took his first full coaching role in July 2012 at amateurs Rieti of Eccellenza Lazio, then resigning later in November 2012 for personal reasons.

[8] Di Napoli undertook his first move abroad in late 2014, when on 31 January 2014, he signed for Maltese club Vittoriosa Stars, in view of the 2015 remaining season.

He was successively named head coach of Serie D club Messina in August 2015, but was forced to quit in February 2016 after being disqualified for four years due to his involvement in the 2015 Italian football scandal.

[11] His disqualification ended officially on 12 July 2019, on which day he announced he was in talks to become head coach of amateur club Cologno.