João Paulo transferred permanently to Santa Cruz in 2016 before being signed by Botafogo, where he played for three seasons and made 68 appearances, scoring five goals.
[3][4] On 31 January 2020, João Paulo was signed on loan by Seattle Sounders FC of Major League Soccer to a Designated Player contract.
[6] In his first MLS season with the club, which was shortened due to the COVID-19 pandemic, João Paulo made 19 appearances, including 17 starts, scoring two goals and recording five assists as a deep-lying playmaker.
[11] João Paulo was named to the five-candidate shortlist for the Landon Donovan MVP Award for his 11 assists and defensive performances, which helped the Sounders qualify for the playoffs despite a depleted roster.
[12] He played through Seattle's run to the 2022 CONCACAF Champions League Final, where he started in both legs as the Sounders won their first continental title.