His managing career started at Atlanta between 1961 and 1963, he led the team to two respectable finishes in the league. He then had an unsuccessful stint on the managing team of the Argentina national team in 1965.
Estudiantes
His managerial career took off with Estudiantes de La Plata. He was hired by the club in 1965 to help the team stave off relegation; he combined many prospects from Estudiantes' la tercera que mata ("the killer juveniles") with a small number of outside talent, and built one of the most successful teams in the history of Argentine football.
The first championship of the so-called "Golden Era" came in 1967, when Estudiantes became the first "small" team to win an Argentine championship. The team came back from three goals down to beat Platense in the semifinal 4–3, then took the crown with a convincing 3–0 victory over Racing Club.
Estudiantes then took second place in the Nacional championship, qualifying for the 1968 Copa Libertadores, which Estudiantes won after defeating Brazilian side Palmeiras.
On 17 January 1982 Zubeldía died of a heart attack in Medellín, Colombia at the age of 54, while setting a bet on horse race.
Legacy
Zubeldía's legacy was carried to fruition by the key tactical player of his Estudiantes, Carlos Bilardo, who went on to become one of the most successful coaches in Argentine history. Bilardo dedicated to his mentor both the 1982 Metropolitano title won by Estudiantes and the 1986 FIFA World Cup title won by Argentina.