In June 2002, Benfica signed him on a four-year deal, with Diogo Luís and Toni going in the other direction on loan deals. From early on, Cristiano struggled with competition from Ricardo Rocha, and on occasions, Cabral. He only made his debut on 3 November 2002 against Santa Clara, but with the arrival of José Antonio Camacho, he began playing much more frequently, finishing the season with 14 appearances. The following season, Cristiano was set to reunite with Jesualdo Ferreira at Braga, but the loan deal fell through. Still, Cristiano started 8 league games in the first half of the season, until the arrival of Fyssas in January. From then on, he became a bench player and never returned to the starting eleven. In May, he added his second trophy in Portugal, after winning the 2003–04 Taça de Portugal.
