Following a discussion with teammate Freddie Freeman, who was diagnosed with COVID-19 before the 2020 season began, Markakis initially decided to opt out of the 2020 season. On July 29, however, Markakis announced that he planned to rejoin the Braves. He was added to the team's active roster on August 5. Markakis was placed on the injured list on August 18, due to potential exposure to COVID-19 while not with the team. He was reactivated on August 25. In 2020 he batted .254 (a career low)/.312/.392 with 15 runs, one home run, and 15 RBIs in 130 at-bats.