In 1992, he moved to Bari, and after two seasons in Serie B, he helped his team to achieve Serie A promotion. During the 1994–95 season, he scored his first goal in Serie A against Napoli, as well as his first ever hat-trick, against Lazio. He came to more widespread notice during the 1995–96 Serie A season, in which he shared the top-scoring title with Giuseppe Signori, scoring 24 goals (including a brace against Inter), despite his team, Bari, being relegated. This achievement led to a move to Lazio in 1996, but Protti's stay with the Rome club was not successful, and after two seasons with the club, including a loan to Napoli during the 1997–98 season, he was eventually released from his contract in 1998.