He won the Coppa Italia over Parma in his first year, scoring in a 1–1 draw in the second leg of the final at home, which allowed his team to clinch the title 2–1 on aggregate;[11] however, his second season was less successful, as financial collapse by the Viola and their subsequent relegation precipitated a 2002 return to his previous club on a four-year deal as a free agent.

[12][13][14] A series of injuries limited Gomes to under 70 games from 2002 to 2005,[15][16] but he still helped Benfica win the domestic cup in 2003–04 and the league the following season – in the latter, he contributed seven goals from 23 appearances.

[18] From 2006–07 onwards, Gomes faced tough competition for a starting place: he only netted six times in the league, and would suffer even more after the signing of Paraguayan Óscar Cardozo the following summer.

[19] On 2 October 2008, Gomes scored his 150th goal for Benfica in a UEFA Cup game against Napoli (2–0 home win, 4–3 aggregate victory) with a fine header.

[23] In two consecutive league games in March 2011, he scored three goals, one at home against Portimonense (1–1 draw)[24] and two in a 5–1 away rout of Paços de Ferreira, appearing as a late substitute in all three matches.

[25] Gomes was released by Benfica on 30 June 2011, after the club decided not to renew his contract; he was, however, offered a position in the managerial structure, effective immediately or when he eventually retired.

[31] On 18 August he made his league debut for his new club, against Ipswich Town,[32] scoring his first goal the following round in the 2–1 home victory over Leicester City.

[43] Things went better for Gomes at Euro 2004, where he played each game and, after coming on as a half-time substitute, scored the winning goal against Spain to send the hosts through to the quarter-finals.

[48] On 7 October 2011, after more than two years out of international play, the 35-year-old Gomes replaced Hélder Postiga in the last minute of a 5–3 home victory over Iceland for the Euro 2012 qualifiers.

[53] He spent most of his career in the lower leagues but, from 2004 to 2007, competed in the Segunda Liga with Marco (two seasons) and Olivais e Moscavide (one), totalling 30 games and one goal.