It was in 2004 that Cioni made his breakthrough in sustaining his abilities in time trialing and climbing through important stage races. After a promising Tour de Romandie, where he finished fifth overall, Cioni finished fourth in the Giro d'Italia and followed this up with third place in the Tour de Suisse. Cioni was subsequently chosen to represent Italy at the World Cycling Championships, however, was not allowed to complete when he registered a hematocrit level over 50%. Although Cioni was aware his hematocrit level was naturally high, he had failed to get an exemption and personal level from the Italian federation in 1999, since his level was not consistently higher than 50%, but consistently around it. The UCI awarded Cioni an exemption certificate, with a personal level, after further tests in October 2004. In 2005, Cioni moved to the newly formed team where, despite being one of the team's leaders and hence liberated from the role of domestique, he had no notable successes. The best that Cioni achieved at Liquigas was a second place in stage four in the 2005 Giro d'Italia, third place at the 2005 Italian National time trial championships and sixth place overall at the 2006 Tour de Romandie. In 2007, Cioni moved to the Belgian ProTour team . His first victory with this team came when he won the first stage of that year's Vuelta a Andalucía, outsprinting his breakaway companion Antón Luengo.