[1] San José started his coaching career with Ekintza Ikastola, and joined Real Sociedad's youth teams in 2008, from Antiguoko.

[5] In July 2014, San José was named Al-Ettifaq FC manager in the place of Ioan Andone, but was sacked the following 17 February.

[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.

[13] On 24 June 2019, San José returned to Europe after being named manager of Belgian club KAS Eupen.

[20] On 17 February 2025, San José returned to his home country after being manager of Segunda División side SD Eibar, replacing sacked Joseba Etxeberria.