He spent the better part of his professional career with Athletic Bilbao, appearing in 242 competitive matches and scoring 11 goals while winning the 2015 Supercopa de España.

[13] On 16 September, he took the first touch at the new San Mamés Stadium against RC Celta de Vigo and scored the 3–2 winner; he was substituted to a standing ovation, and dedicated his performance to his grandparents.

[16][17] In July 2020, Athletic confirmed that Beñat'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 (along with long-serving colleague Mikel San José, also leaving in similar circumstances)[18][19] was acknowledged at the last home fixture on 16 July 2020 in an empty San Mamés[20]– he was in the matchday squad but did not leave the bench, with his last appearance five months earlier;[21][22] he had been involved in the side's run to the Spanish Cup final, 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.

He made his debut for the full side on 26 May 2012, playing 45 minutes in a 2–0 friendly win with Serbia in St. Gallen[25] and thus becoming the first Betis player since Juanito to don the national team shirt, nearly four years later.