In October 2000 he was surprisingly appointed by Genoa chairman Gianni Scerni to replace Bruno Bolchi at the helm of the rossoblu in the Serie B. Carboni, lacking a valid coaching license for heading a Serie B club, guided the club jointly with veteran manager Alfredo Magni, but was sacked in January 2001 following a poor 17 points in 15 matches.
In 2001-2002, Carboni was appointed at the helm of ambitious Serie C1 side Pisa, but failed to lead the club to a promotion spot, ending the season in a poor tenth place.
After Bari replaced him with Rolando Maran during the summer, he started the 2006-07 season without a job, being appointed in February 2007 as new Crotone boss following the dismissal of Elio Gustinetti in an attempt to avoid relegation which later proved to be unsuccessful.
[6] In April 2009 he was appointed to replace Elvio Selighini at the helm of relegation-battling Serie B side Rimini,[7] however failing to save his team from falling down to the lower tier after being defeated to Ancona in the relegation playoffs.
On 25 April 2010, Frosinone announced that Carboni would be the new manager after a poor string of results led to the sacking of Francesco Moriero,[8] leading the club to safety.