On 10 August 2017, De Roon re-signed for Atalanta for an undisclosed fee. He once again cemented himself as a starter under Gian Piero Gasperini, and helped Atalanta finish in a historic 3rd place in the 2018–19 season, earning them a spot in the 2019–20 UEFA Champions League group stage. He also scored a volley against Fiorentina in the Coppa Italia semi-finals in the 58th minute. Atalanta would win the tie 5–4, though lost in the final against Lazio. He made his Champions League debut on 18 September 2019 against Dinamo Zagreb.