After a spell in Serie B at Reggiana (1998–99), helping the club to Serie A promotion, Protti returned to Livorno in Serie C1 in 1999, where he rapidly became one of the most popular players in that club's history, scoring 11 goals during his first season with the club. He later captained Livorno, leading the club to Serie B promotion during the 2001–02 Serie C1 season, winning the title, and finishing the campaign as the top-scorer, and the following season he was the top-scorer in Serie B. He subsequently led Livorno to Serie A promotion during the 2003–04 season, before retiring in 2005 after the team had finished a surprising 9th in their first top division campaign in many years, leaving the captain's armband to Cristiano Lucarelli. Protti's number 10 was then retired by the club. He has also been given the freedom of the city of Livorno in 2007. During the awarding ceremony, he asked the #10 jersey not to be retired any longer in order to "give anybody back the dream to dress it one day". The number will be reassigned starting from the 2007–08 season, with Francesco Tavano wearing the number 10 shirt.