On 6 June 2016 Jean Mota signed a four-year deal with Santos. He was officially announced at the club three days later. He made his debut for Peixe on 26 June, coming on as a late substitute for goalscorer Lucas Lima in a 3–0 home win against São Paulo.
Jean Mota scored his first goal in the main category of Brazilian football on 24 July 2016, netting the winner in a 3–2 success at Vitória. He made his Copa Libertadores debut on 19 April of the following year, starting as a left back and being sent off in a 0–0 away draw against Independiente Santa Fe.