[3] Matheus made his professional debut on 18 September 2012, coming on as a second-half substitute for field player Fábio Júnior as starter Neneca was sent off, in a 2–0 away loss against Clube Atlético Bragantino in the Série B.

[6] He made his Primeira Liga debut on 27 September in a 3–0 home win over Rio Ave FC,[7] and finished his first season as starter ahead of Stanislav Kritsyuk and compatriot Victor Golas after being delayed by bureaucratic problems.

[10] He made his continental debut in that same season's UEFA Europa League, appearing in 12 games and only receiving a yellow card in the quarter-final elimination away to FC Shakhtar Donetsk on 14 April, after conceding a penalty through a foul on Viktor Kovalenko.

[18] In the following campaign's Europa League, Matheus made two saves in a penalty shootout win over FC Sheriff Tiraspol in the knockout round play-off on 24 February 2022,[19] and days after the last-eight elimination by Rangers in April he extended his contract to 2027.

[22] On 15 August 2023, Matheus surpassed compatriot Alan's record of 63 games for Braga in European competition, in a 4–1 away win over Serbia's FK TSC in the third qualifying round of the UEFA Champions League.