Born in Cuiabá, Mato Grosso, Natanael made his senior debuts with Operário de Várzea Grande in 2009.

In 2011, he joined hometown's Cuiabá, after a short stint at Associação Atlética Serra [pt] de Tangará.

[2][3] On 19 December 2013, after his contract with Cuiabá expired, Natanael signed a one-year deal with Série A club Atlético Paranaense.

The Brazilian quickly established himself as a first choice in the main squad, helping Ludogorets to win their fifth championship in the 2015–16 season.

Natanael then played in all 6 qualifying matches of the 2016–17 UEFA Champions League, with his team managing to enter the group stage of the tournament.