In 1999, he was signed by Fiorentina for 28 billion lire (€14.46 million), a team looking to expand and bring in better players, in an attempt to keep club captain and talisman Gabriel Batistuta. Despite making regular appearances in his first season for La Viola, Chiesa was fighting for a place with Predrag Mijatović among others, and also had spells where he was out of form, and in the end only managed 6 goals in the League. In the 2000–01 season, Batistuta left for Roma and Fiorentina were plagued with injuries and financial problems. Meanwhile, Chiesa became the main striker for the club under manager Roberto Mancini, supported by playmaker Rui Costa, and scored 22 goals in 30 matches, finishing amongst the top 5 highest scorers in the league and helping Fiorentina to win the 2000–01 Coppa Italia over his former club, Parma, in the final; in the second leg at home, he set up Nuno Gomes's goal in a 1–1 draw, which allowed Fiorentina to clinch the title 2–1 on aggregate. The 2001–02 campaign proved to be a very difficult one: Chiesa started the campaign off strongly, scoring five goals in the first five matches of the season, but was ruled out for the rest of the season after sustaining a serious injury to his knee ligaments against Venezia on matchday five; left without Chiesa to lead the club's attack, Fiorentina were ultimately relegated at the end of the season. As a result of Fiorentina's relegation and financial troubles, Chiesa subsequently moved to Lazio for the following season, where he however failed to play at his personal best.