Following the start of the season, Costa would suffer a serious injury which would keep him out of action for three months. Costa returned in January 2007, in a Taça de Portugal fourth round tie against Oliveira do Bairro S.C.. Following his return, he was used as a regular in Benfica's starting XI under manager Fernando Santos. His first season would see Benfica finish behind rivals Porto and Sporting CP in the Primeira Liga. In other competitions Benfica participated in, the club would be eliminated in the round of 16 in the Taça de Portugal and bow out of the UEFA Cup against Espanyol.