San José started his coaching career with Ekintza Ikastola, and joined Real Sociedad's youth teams in 2008, from Antiguoko.[1] In August 2012, he moved abroad, being named manager of the under-21 team of Al-Ittihad FC.[3]
In February 2013, San José replaced compatriot Raúl Caneda at the helm of the first team,[4] and finished the campaign in seventh; at the Kings Cup he led the club to the eight cup title of their history, and at the age of 33, he became the youngest manager to lift a trophy in Saudi Arabia.[1] On 1 December, however, he was sacked.[5]
On 22 May 2016, San José switched teams and countries again, after being appointed manager of Club Bolívar.[8] On 20 December of the following year, he resigned,[9] and was announced as Universidad Católica manager the following day.[10]
On 10 December 2018, after lifting the year's Primera División trophy, San José left the UC,[11] and joined Al-Nasr SC five days later.[12] He was sacked the following 1 April, after a string of poor results.[13]
On 24 June 2019, San José returned to Europe after being named manager of Belgian club KAS Eupen.[14] On 27 April 2021, he left the club after opting to not renew his contract.[15]
On 18 May 2021, San José was appointed as manager of Liga MX club Mazatlán.[16] He was dismissed the following 2 March, with the club in the 14th position.[17]
On 12 November 2022, San José agreed to return to Bolívar, replacing Antônio Carlos Zago.[18] He resigned on 19 November 2023 after being touted to return to Mexico,[19] five days later, Atlas announced him as manager for the 2024 Clausura.[20]
^ abcd"Beñat, rey de Arabia" [Beñat, king of Arabia] (in Spanish). Noticias de Gipuzkoa. 7 July 2013. Archived from the original on 10 July 2013. Retrieved 5 September 2019.