Born in Teresina, Piauí, Matheus Felipe joined Mirassol's youth setup in 2014, aged 15.[1] Known as Matheus Piauí at the time, he made his senior debut on 23 July 2017, coming on as a second-half substitute in a 0–1 away loss against Penapolense, for the year's Copa Paulista.
On 7 April 2021, still owned by Prudente, Matheus Felipe signed for Série B side CSA until the end of the year.[4] He immediately became a starter for his new side, only missing out two league matches due to suspension as his side narrowly missed out on promotion.
On 3 December 2021, Matheus Felipe signed a five-year contract with Athletico Paranaense for the 2022 campaign.[5]