Romagnoli made his first appearance of the 2016–17 season in a 3–2 victory in Serie A against Torino. On 23 December, Romagnoli helped lead Milan to victory in the Supercoppa Italiana, playing the full 120 minutes as Milan beat Juventus 4–3 in the penalty shoot-out following a 1–1 draw after extra time. On 15 April 2017, Romagnoli scored his first ever Serie A goal for Milan in the Derby della Madonnina.