[2] He made his senior debut on 22 August 2017, starting in a 2–0 home defeat of Tiradentes, for the year's Copa Fares Lopes.

[3] 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.

[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.

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.