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.
His managerial career took off with Estudiantes de La Plata. Hired in 1965 to help 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.
Zubeldía was a harbinger of tactical changes; he was the first manager to thoroughly research rival team's tactics and playing style. Pre-planned plays off free kicks and tactical fouls to stop rival advances were highly criticized at the time, but have since been adopted by virtually every team in the world. So are other practices, like the offside trap (having the defense step forward in sync to force opposing players into an offside position) and using screens at corner kicks.
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.