On 13 September 2020, Nathan moved abroad for the first time in his career, after agreeing to a one-year loan deal with Primeira Liga side Boavista,[4][5] with an obligation to buy.

[6] He made his professional debut thirteen days later, replacing Jesús Alejandro Gómez late into a 5–0 home loss to FC Porto.

[8] He established himself as a regular during the 2021–22 campaign, and scored his first professional goal on 16 December 2021, netting his team's fourth in a 5–1 home routing of Braga, in the Taça da Liga.

[9] On 5 August 2022, Nathan returned to his home country after signing a contract with Série A side Santos until December 2026.

[11] On 27 June 2023, Nathan was fined 50% of his wages and separated from the first team squad due to disciplinary reasons, being also transfer-listed by the club.