On 23 June, Baroni became the head coach of Novara Calcio. He guided the club to a promotion playoff spot, but was not confirmed by the club for the new season and was successively appointed as new head coach of freshly-promoted Serie B club Benevento. In his first season in charge, he led Benevento to fourth place in the regular season and to ultimately win the promotion playoffs after winning a two-legged final against Carpi, thus bringing the Campanian club to Serie A for its first time ever. He was confirmed as Benevento head coach for the 2017–18 Serie A season. He was sacked on 23 October 2017.