In the 2019–20 season, under new manager José Mourinho, Sissoko scored his first goal in over two years in the match against Bournemouth. This is only his second Premier League goal for Tottenham and helped the team to a 3–2 win. In the 2020 New Year's Day match against Southampton, Sissoko damaged the medial collateral ligament of his right knee, which required surgery resulting in him being out of action for more than three months. However, due to the COVID-19 pandemic which resulted in the suspension of League matches, he did not play any game until the 19 June match against Manchester United after the season restarted.