Born in Santos, São Paulo, Emerson finished his formation in local Santos' youth categories, and made his first team debut on 21 January 2012, against XV de Piracicaba. In February, he returned to youth team, but in March he won a new chance and was related to the match against Mogi Mirim. He also appeared against Ituano and Paulista, as the club was crowned champion for the third consecutive time.
On 17 June, Emerson made his Série A debut, in a 0-1 defeat against Flamengo. He scored his first goal on 5 September 2013, but in a 1–2 loss at Atlético-PR.