At the start of the 2007–08 season, Naldo continued to remain in the first team spotlight, where he formed a partnership with Per Mertesacker. Naldo played in both of the UEFA Champions League Play–Off Rounds against Dinamo Zagreb, as Werder Bremen won 5–3 on aggregate. During a 3–0 loss against Borussia Dortmund on 14 September 2007, he was involved in a legal action by the opposition team after he was kicked Jakub Błaszczykowski, but avoided consequences. It wasn’t until on 27 October 2007 when Naldo scored his first goal of the season in a 1–1 draw against Schalke 04. This was followed up by helping the club keep four clean sheets in the next four matches domestically, and scored against Karlsruher along the way. However, he was sent–off in the 70th minutes for a professional foul on Stanislav Šesták, as Werder Bremen lost 2–1 against VfL Bochum on 3 February 2008. Following this, Naldo served a two match suspension. Amid to his suspension, he played in both legs of the UEFA Cup Round of 32 against Braga and scored in the first leg, as his contributions saw the club through to the next round following 4–0 win on aggregate. The following month, Naldo was involved in an incident at training after clashing with Boubacar Sanogo, but Werder Bremen’s manager Schaaf played down the incident. Naldo scored his fourth goal of the season and set up a goal for the club’s first goal of the game, in a 6–1 win against Hannover 96 on 10 May 2008. On the last game of the season against Bayer Leverkusen, he helped the club win 1–0, resulting in Werder Bremen finishing second place in the league, as well as, the club qualifying for the UEFA Champions League qualifying next season. In his third season at Werder Bremen, Naldo played in all but two of the club’s Bundesliga games in the 2007–08 season, due to suspension, and in all their Champions League fixtures, along with two in Champions League qualifiers, making a total of forty–seven appearances and scoring four times in all competitions. For his performance, he was named 2007–08 season’s kicker Team of the Season for the second time.