[2] Born in Capão da Canoa, Rio Grande do Sul, Jonathan joined Internacional's youth setup in 2009, aged ten, after two years at Juventude.
Jonathan made his first team – and Série A – debut on 2 September 2019, coming on as a second-half substitute for Brenner in a 1–0 away win against Fluminense.
[6] On 9 August 2023, Jonathan made his first career move abroad to join Polish third tier club Kotwica Kołobrzeg on a two-year deal.
He was the league's best goalscorer across the regular season,[8] as Kotwica finished 2nd in the standings and were promoted to the I liga for the first time in the club's history.
[13] On 17 January 2025, Jonathan signed with Ekstraklasa club Radomiak Radom on a six-month contract with a one-year extension option.