At the start of the 2006–07 season, Naldo started the season well when he started two matches in the DFL-Ligapokal to win the tournament, including a 2–0 win against Bayern Munich in the final. Since the start of the 2006–07 season, Naldo continued to establish himself in the first team, playing in the centre–back position. He then helped Werder Bremen kept three clean sheets in three matches between 30 September 2006 and 18 October 2006, and scored two goals against Bochum and Levski Sofia along the way. A week later on 27 October 2006, Naldo scored his third goal of the season, in a 6–1 win against Mainz 05. Naldo scored a hat-trick against Eintracht Frankfurt, which ended as a 6–2 win for Werder Bremen on 9 December 2006 and became the only defender to score a hat trick in the Bundesliga. This was followed up by scoring his seventh goal of the season, in a 2–1 win against Wolfsburg. It wasn’t until on 14 February 2007 when he scored his eighth goal of the season, in a 3–1 win against Ajax in the first leg of UEFA Cup Round of 32. In the return leg, Naldo helped the club reach the next round despite losing 3–1 in the second leg. He then helped Werder Bremen kept six consecutive clean sheets between 14 March 2007 and 8 April 2007, including two UEFA Cup matches against Celta de Vigo and AZ Alkmaar. Naldo played in both legs of the UEFA Cup semi–finals against Espanyol, as the club lost 5–1 on aggregate. On 10 May 2007, he signed a contract extension with Werder Bremen, keeping him until 2012. With the club chasing the league title, Naldo, however, scored an own goal, in a 2–1 loss against Eintracht Frankfurt, putting Werder Bremen out of the title race and went on to finish third place in the league, resulting in the club’s UEFA Champions League qualifying next season. Just as in his first season, Naldo played in all but two of Bremen's Bundesliga games in 2006–07 season, as well as in every European fixture, making a total of forty–nine appearances and scoring eight times in all competitions. For his performance, he was named 2006–07 season’s kicker Team of the Season.