 Zapata began the 2018–19 season with injury, and was third-choice centre-back behind Musacchio and Alessio Romagnoli.His first appearance of the season came on 4 October, in Milan's second Europa League match, a 3–1 at home to Olympiacos.Zapata started the club's final five matches in Europe, including their final match away to Olympiacos, in which Zapata scored at both ends in the second half, two minutes apart.