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.
On 1 October 2019, Zapata scored Atalanta's first ever goal in the UEFA Champions League in a 2–1 loss against Shakthar Donetsk.
On 30 May 2019, Zapata was included in the 23-man final Colombia squad for the 2019 Copa América. In a pre-tournament friendly on 9 June he scored his first international goal at the end of a 3–0 win away to Peru, having replaced Radamel Falcao at half time. He then scored in the first two group games in Brazil, against Argentina (2–0) and Qatar (1–0).