On 19 December 2013, after his contract with Cuiabá expired, Natanael signed a one-year deal with Série A club Atlético Paranaense.[4] He made his debut in the competition on 20 April, starting in a 1–0 home win against Grêmio.[5] On 3 July 2014, Natanael signed a new three-year deal with Furacão.[6] He finished the campaign with 31 appearances (all starts), also appearing regularly during the year's Copa Libertadores.
In July 2015, Natanael signed for Bulgarian champions PFC Ludogorets Razgrad for an undisclosed fee.[7] On 8 August, he played 55 minutes for Ludogorets II in a B Group match against Vereya. Natanael made his first-team debut on 16 August, playing the full 90 minutes as Ludogorets beat Lokomotiv Plovdiv 1–0 at Ludogorets Arena. 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. On 28 September 2016, he opened the scoring in the home match against Paris Saint-Germain in the group stage, netting from a free kick, but the Razgrad team went on to concede three goals and lost the match.[8]