On 21 August 2007, Milan officially confirmed the transfer of Emerson for €6 million. He made his Milan debut in the club's 3–1 UEFA Super Cup victory over Sevilla on 31 August. However, Emerson was unable to contribute significantly to his new club due to injury, only managing 20 appearances for Milan in the 2007–08 season. Nonetheless, he was also able to win the 2007 FIFA Club World Cup with Milan. On 21 April 2009, he and the club mutually agreed to terminate his contract.