On 16 July 2017, N'Jie made his move to Marseille permanent, signing for an undisclosed fee. On 6 August, in the season opener against Dijon, he came on at half time for injured captain Dimitri Payet and scored two goals in a 3–0 win. On 17 September, he scored both the goals in the away win over Amiens. On 3 May 2018, he played in the Europa League semi-finals away to FC Red Bull Salzburg as Marseille played out a 2–1 away loss but a 3–2 aggregate win to secure a place in the 2018 UEFA Europa League Final.