José Mourinho's FC Porto paid €3 million to bring Nuno back to the country in July 2002, as part of the deal that saw Jorge Andrade join Deportivo. During a 2003 Taça de Portugal match against Varzim SC, he was allowed by Mourinho to convert a penalty kick, scoring the club's last goal in a 7–0 home routing. In May 2004, Nuno was an unused substitute as Porto won the UEFA Champions League final. On 12 December 2004, he replaced club great Vítor Baía during extra time of the Intercontinental Cup final penalty shootout victory against Once Caldas; however, in January, he was sold to Russian Premier League's FC Dynamo Moscow.