Naldo made his competitive debut for the club, starting the whole game, in a 5–0 win over Schönberg 95 and setting a goal for Ivica Olić, who would score a hat-trick in the first round of DFB-Pokal. He made his league debut for Wolfsburg, starting the whole game, in a 1–0 win over Stuttgart in the opening game of the season. Since joining the club, Naldo quickly established himself in the starting eleven, playing in the centre–back position.However during a 3–0 loss against Bayern Munich on 25 September 2012, he suffered a bruised ribs that saw him substituted in the 67th minute. But Naldo made a quick recovery and returned to the starting line–up against Mainz 05 on 30 September 2012. However, his performance was criticised by manager Felix Magath. Shortly after the criticism, Magath would be sacked after only five points in eight matches (and no goals and points in the last four games). On 18 November 2012, he scored his first goal for the club in a 3–1 win over TSG 1899 Hoffenheim. Three weeks later on 8 December 2012, Naldo scored his second goal for Wolfsburg, in a 3–2 win against Borussia Dortmund. He later scored three more goals later in the 2012–13 season, coming against Augsburg , Mainz, Hoffenheim and Borussia Dortmund. Despite missing out three matches, due to a hamstring injury in the 2012–13 season, Naldo finished his first season at the club, making thirty–six appearances and scoring six times in all competitions.