After the 1998 World Cup, Baggio signed with his favourite childhood club Inter Milan in order to compete in the UEFA Champions League. After injuries, disappointing results, and several managerial changes throughout the season, including Luigi Simoni, Mircea Lucescu, and Roy Hodgson, Baggio struggled to gain playing time, and was used out of position as a winger, often as a substitute. Baggio scored 5 goals and provided 10 assists in 23 appearances during the 1998–99 season, as Inter finished in eighth place, missing out on a European spot. He helped Inter to a Coppa Italia semi-final, losing out to eventual winners Parma. Baggio scored a goal against his former club Bologna in a European play-off match, but Inter lost both matches, failing to qualify for the UEFA Cup. Baggio also scored four goals in the Champions League, helping lead Inter through the qualifying rounds to the quarter-finals, where they were eliminated by eventual winners Manchester United, also scoring a memorable brace against defending champions Real Madrid in the group stage.