Nkoulou played his first official match for Lyon at the Trophée des Champions, making his first start, in a 4–1 loss against Paris Saint–Germain. A week later, he made his league debut for the club, in the opening game of the season, in a 3–0 win over Nancy. In his first match against Marseille for the first time, which saw them drew 0–0 on 18 September 2016, Nkoulou received boos from Marseille supporters during the match every time he touched the ball. Around the same time he was competing with Mouctar Diakhaby, Nkoulou's performance soon came under criticism by observers, prompting Manager Bruno Génésio defended him.