Conte began his career with the youth team of his hometown club Lecce and made his Serie A debut with the first team on 6 April 1986, aged 16, in a 1–1 draw against Pisa. Under manager Carlo Mazzone, he became a fundamental player for the squad. In 1987, he fractured his tibia, running the risk of a career-ending injury. However, during the 1988–89 season, he was back on the pitch, and scored his first Serie A goal on 11 November 1989 in 3–2 loss to Napoli. He amassed a total of 99 appearances and 1 goal for Lecce.