After failing to appear in Fiorentina's opening five league matches under new manager Giovanni Trapattoni the following season, Morfeo was sent on loan to Italian giants Milan in 1998, who had been impressed by the youngster's performances the previous season; however, his time at the Milanese club was largely unsuccessful, as several injuries and disagreements with manager Alberto Zaccheroni limited his playing time, and he only managed to obtain eleven appearances, mostly as a substitute, scoring one goal. Furthermore, Milan's rigorous use of the 4–4–2 system and subsequent switch to a 3–4–3 formation, neither of which featured an attacking midfielder, meant that Morfeo was often forced to play out of position as a winger, where he was not as effective or influential to the team's attacking play; as a result, he was often benched. Despite his mixed success throughout the season, he still managed to win his only professional trophy with the club that year, as Milan finished the 1998–99 season by claiming the Serie A title.