After starting out at Liverpool's reserves San José joined Athletic Bilbao in 2009, initially on loan, and went on to make 397 competitive appearances for the club (winning the 2015 Supercopa de España) before his departure in 2020.

[24][25] 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.

[26] He also netted the opening goal of a 4–0 win against FC Barcelona in the first leg of the 2015 Supercopa de España, striking from 46 metres (50 yd) after a clearance from opposing goalkeeper Marc-André ter Stegen.

[10] 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.

[28] 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.

On 21 September 2020, San José signed a two-year deal with English Championship club Birmingham City, whose head coach was fellow Basque Aitor Karanka.

[39][40][41] Under new head coach Lee Bowyer, he seemed back to his best in a second-half cameo away to Derby County as Birmingham avoided relegation,[42] but on 28 May, his contract was terminated by mutual consent at his own request.

[48] He made his debut on 4 September, featuring the full 90 minutes in a 0–1 friendly loss to the former,[49] and was subsequently selected for the UEFA Euro 2016 tournament alongside Athletic teammate Aritz Aduriz.