Marquinhos missed PSG's victory in the 2016 Trophée des Champions in August due to his selection in the Brazil team at the Olympics. He was tipped by ESPN journalist Jonathan Johnson to play more frequently over the season, as new manager Unai Emery sold David Luiz back to Chelsea. He scored his first goal of the season on 26 February 2017, opening a 5–1 win at rivals Marseille; prior to the game he confirmed that he was in talks for a new contract at the club. On 26 April, he scored the last goal of a 5–0 home win over title rivals Monaco in the Coupe de France semi-finals, and he started beside Silva in a 1–0 win over Angers a month later in the final. Marquinhos said on 14 May that there was a "100 percent" chance he would remain at the club the following season.