[3] In June 2008, he was announced as manager of the club in the place of Cabrero; at the age of 27, making him the youngest coach in the history of the Argentine Primera División.

[5] On 8 April 2012, after a 1–1 tie against LDU Quito, the president of Barcelona, Antonio Noboa, entered the dressing rooms, having a strong discussion with the young coach.

Leaving that to the side and not being ego-centric, I choose to step aside for the benefit of the institution, because if the coach and the trainer don't respect each other, there's no project that could work.

[8] On 15 April 2012, Zubeldía returned to his home country after being appointed manager of Racing Club, replacing Alfio Basile.

Zubeldía provided the first team debuts of several youth players which would later establish themselves as regular starters, such as Ricardo Centurión, Rodrigo De Paul, Luis Fariña and Luciano Vietto.

[13] In the 2015 season, Zubeldía led LDU to the first place in the First Stage, but left on 21 December of that year after losing the finals to Emelec.

[18] On 16 June 2017, Zubeldía moved to Europe after being appointed manager of Deportivo Alavés of the Spanish La Liga, signing a one-year deal.

[20] On 3 February 2018, Zebeldía replaced Leonel Álvarez at the helm of Paraguayan Primera División side Cerro Porteño.

[26] He won his first professional title of his career on 28 October 2023, lifting the 2023 Copa Sudamericana after a 1–1 draw (4–3 penalty win) against Fortaleza.

[29] On 20 April 2024, Zubeldía was announced as head coach of Campeonato Brasileiro Série A side São Paulo, signing a contract until December 2025.