Zapata's Serie A season debut came on 7 October, at home to Chievo Verona. However, Zapata would not play regularly until Musacchio picked up an injury against Real Betis on 8 November. Musacchio missed five games due to the injury, but did not regain his place in the Serie A team following his return to fitness. Zapata started seven of Milan's final eight Serie A matches in 2018 following Musacchio's injury, and also started the club's Coppa Italia extra-time win over Sampdoria and their Supercoppa Italiana defeat to Juventus in 2019. Zapata's run in the team came to an end as he picked up an injury early in Milan's first Serie A game of 2019, away to Genoa. He would not be named to a match-day squad for two months, and by the time he returned, Musacchio had cemented his place in the back line alongside Romagnoli. Zapata would get two more starts the rest of the campaign, finishing the season with 20 appearances in all competitions as his contract with the club expired.