Born in Itapetinga, Bahia, Marcos Leonardo moved to Taubaté, São Paulo in May 2014,[2] and joined Santos' youth setup in August, after a trial.

[9] He spent the 2021 campaign as a backup option, initially behind fellow youth graduate Kaio Jorge and subsequently behind new signing Léo Baptistão.

[10] He became an undisputed starter, and started to score regularly for the club in the following years, becoming one of the 50 top goalscorers of their history after a winning goal against Palmeiras on 8 October 2023.

[13] On each of his first three league games for Benfica, against Rio Ave, Boavista and Estrela da Amadora, Marcos Leonardo came on as a substitute during the second half and scored, helping seal 4–1, 2–0 and 4–1 victories, respectively.

[14][15][16] On 15 February 2024, he made his UEFA Europa League debut, coming off the bench to replace Arthur Cabral in the final minutes of a knockout round play-off match at home to Toulouse; he won a penalty that Ángel Di María converted, allowing Benfica to win by 2–1.