 Despite many problems both inside and outside the pitch, PAOK managed to finish in sixth place in the 2005–06 campaign, with Fernandes appearing in 27 matches as the Thessaloniki club qualified to the UEFA Cup, only to be disqualified shortly after for irregularities.He remained first-choice for the remainder of his spell.On 23 May 2008, after extensive negotiations, PAOK accepted an offer from VfL Bochum, who signed Fernandes for a fee of approximately €1.2 million, with the player reuniting at the German side with former teammate Marcin Mięciel.