At the start of the 2012–13 season, Emanuelson continued to be involved in the first team for AC Milan, alternating between a starting and substitute role. On 3 October 2012 he scored his first goal of the season, in a 2–1 win against Zenit Saint Petersburg in the UEFA Champions League match. A month later on 3 November 2012, Emanuelson scored his second goal of the season, as well as, setting up two goals, in a 5–1 win against Chievo. In the Round of 16 of Coppa Italia, he set up two goals for the side, as the club won 3–0 against Reggina. By November, however, Emanuelson began to find himself placed on the substitute bench. By the time he was loaned out, Emanuelson made twenty appearances and scoring two times in all competitions.