Born in Oliveira, Minas Gerais, Nathan joined Atlético Mineiro's youth setup in 2011, aged 13.
After taking part of the 2017 Florida Cup with the main squad, he made his professional debut on 9 April 2017 by coming on as a first-half substitute for Jesiel in a 1–2 Campeonato Mineiro away loss against Caldense.
[2] He then became a regular starter for the side, and scored his first goal on 8 August by netting the opener in a 4–0 away routing of Paysandu.
[7] Back at his parent club, Nathan immediately established himself in the starting lineup, forming with Junior Alonso the defensive duo of the 2021 Campeonato Brasileiro Série A winning team.
On 20 June 2023, Atlético Mineiro announced that they had reached an agreement with Mexican club UNAM for the transfer of Nathan, with the deal being reportedly worth US$4 million.