Ahead of the 2009–10 season, Naldo was linked with a move to Ligue 1 side Marseille. Amid to his future at Werder Bremen, he helped the club win the German Supercup against VfL Wolfsburg by beating the opposition team 2–1. Naldo started the season well when he scored his first goal of the season, in a 5–0 win over Union Berlin. However, Naldo suffered a thigh injury and missed the first two matches of the opening season. Upon his return, Naldo scored two goals in two matches, with both games a victory against Borussia Mönchengladbach and Hertha BSC. He played in both legs of the UEFA Europa League’s play–offs round against FC Aktobe and scored twice in the first leg, as Werder Bremen won 8–3 on aggregate to advance to the next round. On 10 September 2009, Naldo signed a contract extension with the club, keeping him until 2013, as Manager Thomas Schaaf was delighted to keep the player, even considered him as a key player. He helped Werder Bremen kept five consecutive clean sheets in the league between 13 September 2009 and 17 October 2009. Since returning from injury, Naldo regained his first team place, forming a centre–back partnership with Mertesacker once again. He later added five more goals, including two separate matches against Athletic Bilbao in the UEFA Europa League. Naldo then scored two goals in two matches between 9 February 2010 and 13 February 2010 against Hannover 96 and 1899 Hoffenheim. Two weeks later on 25 February 2010, he scored his thirteen goal of the season to help the club beat Twente in the return leg of the UEFA Europa League Round of 32, having overturned the deficit. On 20 March 2010, Naldo captained Werder Bremen for the first time against Bochum and provided an assist to one of the goals in a 3–2 win. In a follow–up against FC Augsburg, he helped the club reach the final of the DFB-Pokal after beating the opposition team 2–0. In the final against Bayern Munich, Naldo started in the central defence with Per Mertesacker, as Werder Bremen lost 4–0. Despite missing one match during the 2009–10 season, he went on to make forty–eight appearances and scoring thirteen appearances in all competitions. For his performance, Naldo was named 2009–10 season’s kicker Team of the Season for the third time.