Bonaventura made his first appearance for the season in Round 5 of the 2019–20 Serie A season on 26 September 2019, 11 months after his last appearance for the club. On 23 November 2019, he scored his first goal since 7 October 2018 in a 1–1 draw against Napoli. He scored the winner against Bologna in a 3–2 win two weeks later. He was released by Milan at the end of the season, following the expiration of his contract. His last appearance for the club was as a substitute in a 3–0 win against Cagliari at the final day of the season, coming on for Rafael Leão at the 38th minute.