Ahead of the 2011–12 season, Naldo made his return to training for the first time in a year and only "completed a light session with the ball" before being able to return to full training. He made his comeback in mid-August 2011, appearing for Werder Bremen in a friendly match against St. Pauli. A month later on 11 September 2011 against Hamburg, Naldo subsequently returned to Bundesliga action, coming on as a 86th minute substitute, in a late minute 2–0 Nordderby win, which was his first appearance back from injury in sixteen months. Following this, he found himself in and out of the starting line–up in the next seven matches. In an interview with "Kreiszeitung Syke", Naldo said that he was pleased with overcoming his injury nightmare, and felt happy on his return. After missing one match due to a flu, Naldo returned to the starting line–up against Stuttgart on 27 November 2011 and scored his first goal of the season from a free kick, in a 2–0 win. After making three more starts by the end of the year, he injured his knee ligament and was sidelined for months. During the recovery, Naldo was linked with a return to Brazil, as supposedly Internacional and Porto Alegre Futebol Clube were interested in signing him. It came after when he wanted to leave Werder Bremen, citing homesickness. Ultimately, Naldo stayed at the club after being convinced to stay by Manager Thomas Schaaf. By February, he made his return to full training following his recovery on his knee. Naldo made his return to the first team against Mainz 05 on 31 March 2012, coming on as a 51st minute substitute, in a 3–0 loss. After missing one match due to a torn muscle fibre, he scored on his return, in a 2–2 draw against Borussia Mönchengladbach on 10 April 2012. A week later on 21 April 2012, Naldo scored his third goal of the season, in a 2–1 loss against Bayern Munich. At the end of the 2011–12 season, he went on to make eighteen appearances and scoring three times in all competitions.