Born in Japeri, Rio de Janeiro, Jonathan joined Botafogo in August 2017, after already making his senior debut at Nova Iguaçu the previous year.
[1] Initially on loan, he was bought outright and renewed his contract until 2021 in December 2018.
[2] Promoted to the first team for the 2019 season, Jonathan made his senior debut on 26 January 2019, starting in a 2–1 Campeonato Carioca home loss against Flamengo.
[4] Jonathan made his Série A debut on 27 April 2019, playing the full 90 minutes in a 2–0 loss at São Paulo.
On 20 August 2019, Jonathan signed a five-year contract with Segunda División side UD Almería, for a rumoured fee of €1 million.