For four complete seasons in the late 90s/early 2000s, Fernández was in charge of Celta de Vigo, helping the Galicians qualify three times for the UEFA Cup during his spell while playing highly attractive football. From 2002–04 he worked with fellow top flight outfit Real Betis, respectively finishing eighth and ninth in his two years.
Fernández returned to his beloved Zaragoza for the 2006–07 campaign,qualifying the club for the UEFA Cup in his first year but being sacked midway through his second, as the season eventually ended in relegation. In another return he joined Betis in late January 2010, replacing fired Antonio Tapia; during his spell the Verdiblancos were the team in the league with the most points, but they could not eventually promote from Segunda División, after finishing with the same points as the third-placed club.
On 9 January 2013, Fernández moved for his second experience abroad, signing a contract with Belgian side K.A.A. Gent. He was sacked on 30 September 2013 due to poor results.