Born in Francisco Morato in the state of São Paulo, Morato was 18 when he moved from the youth ranks of São Paulo to Benfica in September 2019, on a contract lasting until 2024. The transfer fee was €6 million and the Brazilian club retained 15% of the rights to his next transfer.[2]
On 22 September 2019, Morato made his professional debut for Benfica B in the LigaPro, playing the full 90 minutes of a 1–0 loss at Leixões.[3] He made his first-team debut on 21 December in the final game of the Taça da Liga group stage, again featuring for the entirety of a 2–2 draw at Vitória de Setúbal.[4][5] In the same season, he played 10 games as the under-19 team came runners-up in the UEFA Youth League, scoring in a 3–2 group win at Olympique Lyonnais on 5 November.[6]
On 27 September 2020, Morato scored his first professional goal to open a 2–1 loss for the reserves at Mafra;[7] on 17 October he was sent off in a 1–0 loss away to Arouca.[8] He made his Primeira Liga debut the following 30 April in a 2–0 win at Tondela, as an added-time substitute for Pizzi.[9] On 23 May, he started in the 2021 Taça de Portugal final, lost 2–0 to Braga in Coimbra;[10][11] he had days earlier been told that he would be on the bench for that game.[12]
Morato was given a run in the first team at the start of the 2021–22 season, due to injury to veteran Jan Vertonghen.[13] He scored his first goal for them on 2 November, in the first half of a 5–2 loss at Bayern Munich in the UEFA Champions League group stage.[14] The following season, under new manager Roger Schmidt, Morato earned a place in the starting eleven over Jan Vertoghen, and following a run of four consecutive wins and three clean sheets, he was named the Primeira Liga's Defender of the Month for August.[15]