On 23 August 2015, Bonaventura made his season debut as Milan lost 2–0 to Fiorentina. The following match against Empoli, Bonaventura came on the pitch as the substitute for Suso in the 55th minute and managed to assist Luiz Adriano's winning goal from a corner kick 15 minutes later. On 19 September, Bonaventura assisted Carlos Bacca's first goal and scored directly from a free-kick in a 3–2 win over Palermo. He also gained another assist and goal in Milan's next game, the 2–3 win over Udinese. Once again, he assisted both Carlos Bacca's and Philippe Mexès' goals against Lazio in the 3–1 away win on 1 November. He continued to perform well under the team's coach Siniša Mihajlović and became a fundamental player for his team throughout the season. After missing a 0–0 draw against his former team Atalanta through suspension, he scored the opener in a 4–1 defeat of Sampdoria on 28 November. He scored again in his next game on 1 December, a 3–1 Coppa Italia defeat of Crotone, via a brilliant 20-yard free kick. On 20 December he assisted Carlos Bacca's goal and scored a late goal as Milan beat Frosinone 4–2. On 17 January 2016, he provided another assist for Carlos Bacca as the Rossoneri beat Fiorentina 2–0. He ended the season with 7 goals and 8 assists in all competitions as Milan finished 7th in Serie A, and lost out in the Coppa Italia final against Juventus, following a 1–0 defeat in extra time.