On October 7, 2019, Lowry signed a one-year $31 million extension with the Raptors. On November 2, 2019, Lowry scored a season-high 36 points in a 115–105 loss to the Milwaukee Bucks. On November 8, 2019, Lowry was injured during the 122–102 victory over the New Orleans Pelicans for a sore thumb and sat out for 2 weeks missing 12 games. On December 3, 2019, he made his return against the Miami Heat. He scored 12 points along with 6 rebounds, 11 assists, 1 steal and 1 block in a 121–110 loss. On December 22, 2019, Lowry scored 20 of his game-high 32 points in the fourth quarter in a 110–107 victory against the Dallas Mavericks, helping the Raptors overcome a 30-point deficit, making it their biggest comeback victory in franchise history and the first 30-point comeback win in ten years. On December 23, 2019, Lowry was named Eastern Conference Player of the week for games played between December 16–22. On August 1, 2020, Lowry scored 33 points, along with a career-high 14 rebounds, while leading the Raptors to a 107–93 win over the Los Angeles Lakers. This was the Raptors first game in the Orlando bubble, returning from a 4-month hiatus due to the COVID-19 pandemic. The Raptors were unable to defend their title as they were eliminated in seven games by the Boston Celtics in the second round.