Borgonovo's prolific season with Fiorentina also earned the chance to prove himself with the defending European Cup champions Milan in 1989. He spent much of the 1989–90 campaign as backup to Marco van Basten, also due to injury, only making 13 appearances, and scoring 2 goals, although he helped Milan to capture the European Supercup, the Intercontinental Cup, and most notably, the European Cup that season, first winning a penalty for Van Basten, and then scoring a crucial goal himself in the semi-finals, against Bayern Münich; he scored 2 goals in total in the competition. Despite earning a prestigious European Cup winners' medal, he left the club at the end of the season, keen to play regular first-team football; although Milan coach Arrigo Sacchi was keen to keep his services, he returned to Fiorentina, where he spent two years without managing to recapture his previous form.