After starting his career as a fitness coach, he was appointed Rafael Benítez's assistant at Osasuna, and remained behind the manager at Extremadura, Tenerife, Valencia and Liverpool.
[2][3] Ayestarán joined Real Sociedad as sporting director in 2008, but left after a few weeks due to conflicts with the club president.
[8] On 29 May 2014, after failing to win promotion despite reaching the final of the tournament, Ayestarán announced his departure from Tecos, saying he had "no intention of continuing to manage in the Ascenso MX".
[9] Ayestarán was appointed Maccabi Tel Aviv manager on 26 August 2014, replacing fellow Spaniard Óscar García who had resigned due to the war in Gaza.
[17] He suffered defeat against Las Palmas in his debut match[18] before recording consecutive La Liga wins over Sevilla, Barcelona and Eibar in April.
[26] With a 3–1 home win over Estoril on 21 December 2021, he guided the team to the quarter-finals of the Taça de Portugal for the first time in their history.