Ahead of the 2013–14 season, Naldo said about the new season, saying: "I am convinced that we will be much better. We have to attack, but on the outside we should be a little more cautious. We don't have to talk about it so much, we have to show what our goals are on the pitch." Since the start of the 2013–14 season, he continued to establish himself in the first team, playing in the centre–back position and formed a centre–back partnership with Robin Knoche. Naldo scored his first goal of the season in a 4–0 win over Schalke 04 on 17 August 2013. After the match, he was named the league’s Team of the Week. Naldo scored his second goal of the season, in a 2-1 win over Ingolstadt 04 in the fourth round of DFB-Pokal. Three months later on 8 March 2014, he scored again, which was Wolfsburg's only goal in the game, in a 6-1 loss against Bayern Munich. His performance led to speculation that the club is planning to offer Naldo a new contract. Following the absent of captain Diego Benaglio, Naldo captained Wolfsburg for the first time against Eintracht Frankfurt on 29 March 2014 and scored his fourth goal of the season, in a 2–1 win. Following this, he captained the next four matches until Benaglio return. Despite missing two matches later in the 2013–14 season, Naldo went on to make thirty–eight appearances and scoring four times in all competitions. Shortly after, he signed a new two-year contract extension with the club, keeping him until 2016.