As a manager, he has a long career at the helm of several Serie A and Serie B teams in the whole country. Among the several teams he led, he had his major successes with Atalanta B.C., which he led from Serie B to a ninth place in Serie A, coaching the team for four seasons.
He is often considered a "replacement" coach, as he was often appointed in his career to replace fired managers from Serie A teams fighting to avoid relegation, or Serie B teams which managed to promote.
More recently, Sonetti joined Cagliari on November 2005, replacing Davide Ballardini, becoming the fourth coach appointed by the Sardinian team in a couple of months. He succeeded in maintaining his job until the end of the tournament, and in leading the rossoblù to maintain a place in the next Serie A; he left Cagliari at the end of the season. On November 14, 2006, Sonetti was appointed to replace Attilio Tesser at the helm of then last-placed relegation-battling Serie A Ascoli. He did not manage to save his side from falling to Serie B, and ended his experience in Ascoli at the end of the season with a second-last place. On November 2007 he returned at Cagliari for his third time, as he was appointed to replace Marco Giampaolo at the helm of the Sardinians. He resigned from his post on December 19, but was confirmed by the club the next day after Marco Giampaolo rejected to return at the helm of the club. However, Sonetti was sacked only a few days later, after a 5–1 loss to Fiorentina, leaving the team last-placed in the league table, being replaced by Davide Ballardini. From September 25, 2008, he has been called back to Brescia replacing Serse Cosmi. On May 19, 2009 he was sacked himself, following a 2–1 loss to promotion rivals Grosseto that left Brescia in fourth placed, but with only a two-point lead to 7th-placed Triestina.
On March 28, 2010 69-year old Sonetti returned into management, replacing Rolando Maran as head coach of Serie B relegation battlers Vicenza. His stint as Vicenza head coach, as he was sacked on April 15 after only three games in charge, ended with respectively two draws and a loss.