He made his first appearance of the season in the 2016 Trophée des Champions on 6 August 2016 where Lyon were beaten 4–1 by reigning Ligue 1 champions Paris Saint-Germain. Tolisso himself found the back of the net in the 87th minute but the goal proved to be no more than a consolation. Tolisso scored his first Ligue 1 goal of the season on 27 August, opening the scoring in a 4–2 away loss to Dijon, and his first ever goal (in the 13th minute) in a UEFA club competition on 14 September in a 3–0 UEFA Champions League group stage home win over Dinamo Zagreb.