Born in Pamplona, Navarre, San José progressed through the youth teams at Athletic Bilbao in the neighbouring Basque Country, playing for the Juvenil B and moving to the A-team in the 2006–07 season, where he made 27 appearances and scored five goals. Aged just 18, he signed a three-year contract with Liverpool in August 2007, and subsequently played regularly for the reserves in 2007–08 and 2008–09.
Athletic return
In August 2009, San José returned to Bilbao on a season-long loan, to gain more first-team experience. He was awarded the number 12 shirt, making his debut on 17 September 2009 in a 3–0 group stage home win against FK Austria Wien in the UEFA Europa League. It was reported in early November 2009 that he was frustrated by the lack of first-team opportunities, and that if this did not improve he would look to shorten the loan agreement and move either back to Liverpool or on loan to another club in January 2010; he finally made his La Liga debut on the 8th, playing the last two minutes of the 2–0 away win over Racing de Santander, and finished the campaign with 30 overall appearances, netting three times. On 19 May 2010, San José was signed permanently by Athletic for five years. In his first year he was periodically charged with penalty-taking by manager Joaquín Caparrós, replacing longtime incumbent Andoni Iraola. On 5 December 2010, in his first Basque derby, against Real Sociedad, San José committed a penalty which resulted in the first goal, and scored in his own netin the beginning of the second half, for the game's final 2–0 at the Anoeta Stadium. The following season, he was an unused substitute in the Copa del Rey and the Europa League finals, both lost. San José finished the 2012–13 campaign with six goals all competitions comprised, netting five goals in the league as the Lions finished 12th, and was often utilized as a defensive midfielder by coach Marcelo Bielsa. His other successful strike was his first in a European competition, in a 3–3 draw at HJK Helsinki for the Europa League play-off round second leg. San José scored the first-ever goal for Athletic Bilbao at the new San Mamés Stadium on 16 September 2013, netting from close range in a 3–2 defeat of RC Celta de Vigo. He began to be overshadowed by fellow youth graduate Aymeric Laporte, however. On 25 November 2014, San José scored his first goal in the UEFA Champions League, the only one in a group match away to FC Shakhtar Donetsk – nonetheless, the opponents advanced at Athletic's expense. He also netted the opening goal of a 4–0 win against FC Barcelona in the first leg of the 2015Supercopa de España, striking from 50 metres after a clearance from opposing goalkeeper Marc-André ter Stegen. In September 2019, San José reached the milestone of ten years with the same club. On 24 November, he celebrated his 300th appearance in the Spanish top division in a 2–1 away victory against CA Osasuna, breaking a 31–game undefeated streak of the hosts at their El Sadar Stadium. In July 2020, Athletic confirmed that San José's contract would not be extended beyond that summer, although the departure was delayed beyond its usual June expiry after the season was postponed due to the COVID-19 pandemic in Spain. His contribution was acknowledged at the last home fixture on 16 July 2020 in an empty San Mamés– he was in the matchday squad but did not leave the bench, with his last appearance four months earlier in the Spanish Cup semi-finals; His team won that tie, but the circumstances of the delay and the end of his spell at the club meant he would have no opportunity to take part in the decisive match.
