In October 2019, Jhonnathan signed his first professional contract with the club, until September 2021. He made his first team debut for Peixe on 3 March 2021, coming on as a second-half substitute for Wagner Leonardo in a 1–1 Campeonato Paulista home draw against Ferroviária.[4]
On 19 May 2021, Jhonnathan renewed his contract until April 2026.[5] After failing to appear in any further match for the first team, he was loaned to Série C side Brasil de Pelotas on 20 June 2022.[6]
On 28 November 2022, Santos agreed to loan Jhonnathan to ABC for the 2023 season.[7] He scored his first professional goal the following 8 February, netting the winner in a 1–0 Campeonato Potiguar away success over Força e Luz.[8]