Zebina made his debut for the club, starting the whole game, in a 4–1 win against ND Gorica in the first round of the UEFA Cup. He helped Roma keep a clean sheet in the return leg by beating the opposition team 7–0 to advance to the next round. Zebina followed up by helping the club keep two clean sheets in the next two matches against Bologna and Leece. However, he suffered an injury that saw him missed two matches. But Zebina made his return to the starting line–up against Reggina on 12 November 2000 and helped Roma beat the opposition team 2–1. However, his return was short–lived when he suffered a broken toe during a match against Perugia on 3 December 2000 and was substituted in the 43rd minute, as the club drew 0–0. After a month on the sidelines, Zebina returned to the first team against Bari on 14 January 2001, coming on as a 55th-minute substitute, in a 1–1. However, he found himself on the sidelines on four occasions in the next three months. Despite his absents later in the 2000–01 season, Zebina remained in the first team regular, playing in the centre–back position and helped Roma win the Scudetto. In his first season at the club, he made twenty–six appearances in all competitions.