In the 1999–2000 season, Baggio’s former Juventus manager, Lippi, was appointed as Inter’s new coach. Lippi did not favour Baggio, and left him out of the squad for most of the season, stating that Baggio was out of shape. In his autobiography, Baggio stated that Lippi had dumped him after Baggio refused to point out which of Inter’s players had expressed negative opinions about the coach, also highlighting an incident during a training session, where he called out Christian Vieri and Christian Panucci for applauding Baggio for a notable assist. Baggio was used scarcely, and often as a substitute, scoring only 4 goals in 18 appearances during the regular Serie A season. He made 5 appearances in the Coppa Italia, with his only goal coming against local rivals Milan in the second leg of the quarter-finals, as he helped Inter reach the final, only to be defeated by Lazio. Despite his limited playing time, Baggio still managed several important goals to help Inter to a fourth-place finish, alongside Parma, such as his match winning goal against Verona, which he scored after coming off the bench, after being excluded from the team since 18 December 1999. Baggio had also previously helped to set up Inter’s equaliser during the match. This was the first time Baggio had scored for Inter since his goal on 27 May of the previous season, and in the post-match the interview, he denied accusations made by Lippi in regard to his personal form. Baggio’s last important contribution to Inter was scoring two memorable goals against Parma in the play-off match for the last remaining UEFA Champions League place, which Inter won 3–1; Lippi had been forced to field Baggio due to several injuries. Baggio was given a perfect 10 rating from the Italian sports newspaper La Gazzetta dello Sport, who described his performance as “absolutely perfect all game”. This game is considered an example of professionalism shown by Baggio, as Inter’s president Massimo Moratti had stated that Lippi would only stay on if the team qualified for the Champions League.