A series of nagging injuries limited Gomes to under 70 games from 2002 to 2005, but he still helped Benfica win the domestic cup in 2003–04 and the league the following season – in the latter, he contributed with seven goals from 23 appearances. He enjoyed his best season in 2005–06, scoring 15 goals in the league, including two in an away win over FC Porto (0–2) and a hat-trick against U.D. Leiria, finishing second in the scorers' list and adding the subsequent Supertaça Cândido de Oliveira, where he netted the game's only goal against Vitória de Setúbal.