On 30 January 2019, Zapata scored twice in a 3–0 win against holders Juventus in the quarter final stage of Coppa Italia. After helping Atalanta to reach the 2019 Coppa Italia Final, and achieve a third-place finish in Serie A, and consequently a spot in the Champions League, scoring 23 league goals in the process, Zapata was awarded a spot in the Serie A team of the year at the end of the season.