At the start of the 2011–12 season, Emanuelson played eight minutes after coming on as a substitute, against Inter Milan and helped AC Milan win the 2011 Supercoppa Italiana by beating them 2–1. Since then, he continued to become a first team regular for the club, playing in different midfield positions. Emanuelson then set up AC Milan's only goal of the game, in a 1–0 win against Cesena on 24 September 2011. He then helped AC Milan qualify for the UEFA Champions League knockout stage after drawing 2–2 against Viktoria Plzeň. Emanuelson then played in both legs against Arsenal and helped the club qualify for the next round by winning 4–3 on aggragate. He then scored his first Serie A goal for Milan in an away match against Cesena on 19 February 2012. He scored his second Serie A goal for Milan in an away game against Parma on 17 March 2012. Emanuelson started in every match until he suffered an injury that saw him sidelined for the rest of the 2011–12 season. In his first season at the club, Emanuelson made forty–two appearances and scoring two times in all competitions.