After he missed the beginning of the new season due to mononucleosis, Pongračić returned to the team on 8 November as an injury time substitute for Xaver Schlager in the 2–1 victory over 1899 Hoffenheim. However, on 18 November, he tested positive for COVID-19. On 27 February 2021, he was sent off in the injury time of a 2–0 victory over Hertha Berlin.
