Empoli won promotion to the Serie A in 2002 after finishing in fourth place during the 2001–02 Serie B season with 67 points. They finished with 60 goals, the largest tally in the competition, and Di Natale finished as the club's top goalscorer with 16 league goals. In Empoli's first season back in the topflight, he helped the club fight off relegation by scoring 13 times in the league. This included a hat-trick in Empoli's 4–2 defeat of Reggina on 17 November 2002. The next season was less fortunate for Di Natale, who only scored five goals in the league. Following two seasons in the Serie A, Empoli were relegated back to the Serie B at the end of the 2003–04 campaign.