Valverde's second season in charge was less successful in the league, as Athletic suffered three more losses than the year before and slipped to 9th.[4] They enjoyed more success in the Copa del Rey, reaching the semifinals before being knocked out on penalties by eventual champions Real Betis.
Their European adventure began in the UEFA Cup first round, where they were drawn against Trabzonspor of Turkey. Despite losing the away first leg 3–2,[5] they qualified for the group stage by winning 2–0 at home.[6] They were drawn in Group B, and suffered another defeat in Turkey, this time against Beşiktaş.[7] However, they won their other three games - against Parma of Italy,[8]Steaua București of Romania,[9] and a crushing 7–1 victory over Standard Liège of Belgium[10] - to progress as group winners. Their opponents in the next round were Austria Wien, and despite a creditable 0–0 draw in the away leg,[11] Bilbao were eliminated after a 2–1 defeat at home.[12]
Valverde left his post at the end of the season, and was replaced by José Luis Mendilibar.[13] Mendilibar lasted only until the following October,[14] while Valverde would return to the club for a second spell as head coach in 2013.[15]