After helping Atalanta to gain Serie A promotion during the 1994–95 Serie B season under manager Emiliano Mondonico, Morfeo soon came to prominence with the club during the 1995–96 season alongside Christian Vieri, scoring 11 goals in 30 league appearances, at the age of 19. The following season, he scored less frequently, managing only five goals, but provided several assists for his new attacking partner Filippo Inzaghi; together, they formed a formidable offensive partnership, and Inzaghi finished the season as the league's top-scorer.