Felipe Jonatan was promoted to the main squad for the 2018 season, and was initially a backup to Rafael Carioca and new signing João Lucas. After the arrival of Lisca as new manager, he became the club's first choice,[4] making his debut in the Série A on 6 September by starting in a 2–1 home win against Corinthians.[5]
On 31 October 2018, Felipe Jonatan renewed his contract until May 2022.[6] He scored his first senior goal the following 6 February, netting the opener in a 1–1 away draw against Central, for the year's Copa do Brasil.
Santos
On 1 March 2019, Felipe Jonatan signed a five-year contract with Santos, for a rumoured fee of R$ 6 million.[7] He made his debut for the club the following day, starting in a 3–2 home win against Oeste for the year's Campeonato Paulista.[8]
Felipe Jonatan scored his first goal for Peixe on 28 April 2019, netting his team's second in a 2–1 away defeat of Grêmio.[9] A backup to Jorge during the year, he became an undisputed starter in the 2020 season, after Jorge left.
On 20 April 2023, Felipe Jonatan suffered a knee injury in the early minutes of a 0–0 Copa Sudamericana home draw against Audax Italiano, being sidelined for the remainder of the year.[10] He only returned for the 2024 season, with the club in the Série B, and was a regular starter during the 2024 Campeonato Paulista.
On 17 April 2024, Santos announced the termination of Felipe Jonatan's contract on a mutual agreement.[11]
Fortaleza
On 17 April 2024, Felipe Jonatan returned to his hometown after signing for Fortaleza, a club he already represented as a youth, until April 2027.[12]