The 2005–06 season finished without silverware for Benfica, with Luisão again as an automatic first-choice. However, the team reached the season's UEFA Champions League quarter-finals, with the defender playing all the matches and minutes in the competition. On 21 February 2006, he scored in his side's 1–0 home win against holders Liverpool, which had lost just 1 of 13 European matches the previous year and 5 of 41 away from home. He also started in the second leg, a 2–0 win at Anfield.
In the next year, Luisão was named in the Brazilian squad for the 2005 FIFA Confederations Cup, but did not play a single second, meeting the same fate in the 2006 FIFA World Cup. After the latter tournament, when Dunga was hired as the new coach, he began to play more often.