On 17 June 2013, Santana was named manager of the B-team, signing a two-year deal.[1] On 5 November of the following year, he was appointed at the helm of the main squad, as an interim, replacing fired Jagoba Arrasate.[2]
Santana appeared in his first professional match on 9 November 2014, a 2–1 home win against Atlético Madrid.[3] He was subsequently named David Moyes' assistant, remaining in the first team.[4]
In June 2016, Santana was hired by third-tier Real Unión but still on the payroll of Sociedad, who were helping out with the Irun-based club's financial problems.[5] He was dismissed on 27 November 2017 due to a poor run of results, with the severance payment being again the responsibility of the larger club.[6]
Santana returned to the game on 29 January 2020, taking over at UCAM Murcia until the end of the season.[7]