Manaj debuted for Inter as a substitute in place of Jeison Murillo in a friendly match against Athletic Bilbao on 6 August 2015 won by Inter 2–0. He made his Serie A debut on 23 August 2015 in team's opening match of 2015–16 season, replacing Brozović in the 85th minute of the 1–0 home win against Atalanta. On 15 December, Manaj started for the first time during the Coppa Italia encounter against Cagliari, playing full-90 minutes and providing the assist of the first goal scored by Palacio in an eventual 3–0 win.