On 27 October 2019, Papastathopoulos – marking his 50th appearance – scored his first goal of the season, after Crystal Palace failed to clear Nicolas Pépé's corner in a 2–2 draw at home. On 1 January 2020, he scored a close-range finish to seal a 2–0 win over Manchester United, securing Mikel Arteta his first victory in charge of the "Gunners". He was named Sky Sports Man of the match. On 2 March 2020, he scored with a volley to give Arsenal the lead in a 2–0 away win against Portsmouth, helping Arsenal to be the first team in the FA Cup quarter-finals. On 1 August 2020, Papastathopoulos played as a late substitute in the 2020 FA Cup Final against Chelsea, as Arsenal won the trophy for the 14th time.