Aubameyang scored in Arsenal's 1–1 draw with Crystal Palace on 11 January 2020, but was also sent off for a late challenge on Palace midfielder Max Meyer. Aubameyang was originally given a yellow card for the tackle by referee Paul Tierney, however the card was eventually upgraded to a red card, by the VAR, resulting in Aubameyang's first-ever red card for the Gunners and would mean that the striker would miss Arsenal's next three matches against Sheffield United, Chelsea and Arsenal's FA Cup tie against Bournemouth.
On 29 August 2020, Aubameyang scored a goal in normal time and the fifth and winning penalty in a shoot-out win against Liverpool in the Community Shield, after the game ended 1–1.
On 12 September 2020, Arsenal played their first Premier League game away from home at Craven Cottage against Fulham. Aubameyang scored the third and final goal of the game after a great team effort, he was assisted by Willian. Aubameyang also assisted Alexandre Lacazette's goal in Arsenal's 2–1 win over West Ham United on 19 September.
On 15 September 2020, Aubameyang put an end to months of speculation by signing a new three-year contract with Arsenal. Speaking to the Arsenal website, Aubameyang said: "Signing for this special club was never in doubt, it's thanks to our fans, my team-mates, my family and everybody at this club that I feel like I belong here. I believe in Arsenal. We can achieve big things together. We have something exciting here and I believe the best is to come for Arsenal." On 1 November 2020, he scored a penalty in a 1–0 away win against Manchester United, to grant his team their first Premier League win at Old Trafford since 2006.