[6] In May 1998, Fernández was appointed to replace Javier Irureta at RC Celta de Vigo,[7] Profiting from the recent Bosman ruling, his team fielded many European Union players such as Claude Makélélé, as well as those from further afield such as the Israeli Haim Revivo and Russian midfield duo Valeri Karpin and Aleksandr Mostovoi;[8] the Galician team played highly attractive football and were known as EuroCelta for their performances in continental competitions.

[9] Fernández led Celta in the UEFA Cup in each of his four seasons, reaching the quarter-finals on all but one occasion; highlights included a 3–1 win over Liverpool in November 1998,[10] a 7–0 rout of S.L.

[16] In August 2004, Fernández moved abroad and joined Portuguese club FC Porto; the UEFA Champions League holders had dismissed Luigi Delneri before a single competitive game.

[17] He won on his debut on 20 August in the Supertaça Cândido de Oliveira, with new signing Ricardo Quaresma scoring the only goal of a win against rivals Benfica;[18] on 12 December he added the conquest of the last ever Intercontinental Cup with a penalty shootout victory over Colombia's Once Caldas.

[19] Domestically, Fernández's team gave up their Primeira Liga lead to Benfica on 20 November 2004 when they lost 1–0 at home to neighbours Boavista FC.

[22] Fernández returned to his beloved Zaragoza for the 2006–07 campaign,[23] qualifying the side for the UEFA Cup in his first year but being sacked midway through his second,[24] as the season eventually ended in relegation.