He continued his fine form into the 2015–16 Ligue 1 season where he netted five goals and set up six assists as Lyon ended the Ligue 1 season as runners-up to Paris Saint-Germain. Tolisso's form in the previous season earned him numerous suitors from around Europe and in July 2016 he was subject to a €37.5 million bid from Serie A side Napoli. He turned down the move and reaffirmed his commitment to Lyon, however, citing his affection for the club and belief in their progress as his reasons for staying at the club. 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. On 2 October 2016, with regular captain Maxime Gonalons and vice-captain Alexandre Lacazette injured, Tolisso was handed the armband in their stead and captained Lyon in the first ever Rhône derby against Saint-Étienne at Lyon's new stadium, Parc Olympique Lyonnais. In the return fixture on 5 February, Tolisso received the first red card of his career after being sent off for a foul on Fabien Lemoine in stoppage-time. Just moments before Tolisso's expulsion, Lyon teammate Rachid Ghezzal had been sent off as well for a challenge on the same player. The ill-discipline shown in Lyon's loss to Saint-Étienne prompted club president Jean-Michel Aulas to announce that both players would be severely punished for their actions. Tolisso remained a constant fixture in the side, however, and ended the 2016–17 season with a return of 14 goals and seven assists in 47 appearances across all competitions for Lyon. He was also named in the UEFA Europa League squad of the season. On 14 June 2017, Bundesliga side Bayern Munich secured the signing of Tolisso on a five-year deal from Lyon for an initial transfer fee of €41.5 million, plus up to €6 million in potential bonuses.