In 1997 he joined Cagliari, which he led to a quick return to Serie A.In 1998–99 he finally made his personal Serie A debut, leading Cagliari to a 12th place.During the 1999–00 season, he agreed a return at Sampdoria, this time as head coach, but missed promotion to Serie A ending the season in fifth place.
From 2002 to 2004 he returned at Cagliari: a good ninth place in his first season was however followed by a sacking during the next one.
In 2004–05 he was appointed at the helm of refounded team Napoli, with the goal to achieve immediate promotion to Serie B: however, Ventura did not manage to guide the team to the very top table positions, and he was later fired and replaced with Edoardo Reja.
He returned coaching a Serie A club during the 2005–06 season, when he replaced Bortolo Mutti at the helm of Messina in an unsuccessful attempt to escape from relegation.
In December 2006 he was called by Verona to replace Massimo Ficcadenti; despite a clear improvement in results his club, which was in the bottom of the table at Ventura's appointment time, did not manage to avoid playing a relegation playoff, losing it to Spezia.
Later on June 2007, Ventura was announced as new head coach of newly promoted Serie B club Pisa.