On 15 October 2018, Papastathopoulos was forced off during Greece's 2–0 defeat to Finland and was believed to have sprained his ankle. Papastathopoulos was at the heart of Unai Emery's defense since the Spaniard took over the reins in the summer and a fixture in a winning run of nine matches. On 21 February 2019, he netted his second goal as an Arsenal player, taking advantage of a missed punch from BATE Borisov's goalie Denis Scherbitskiy to head the ball into an empty net following a corner kick from Granit Xhaka, to seal a 3–0 home win for Arsenal and send them through to the Round of 32 in the 2018–19 UEFA Europa League.