Alsogaray was named Under Secretary of the Army in 1962-63, and in 1964, Chief of Gendarmerie, in which capacity he captured the members of an incipient guerrilla group led by journalist Jorge Ricardo Masetti.

Appointed Commander of the 1st Army Corps in January 1966, Alsogaray planned a coup d'état against the democratically elected President Arturo Illia; Illia was a moderate figure who had incurred opposition from conservative groups by refusing to annul Peronist victories in the 1965 mid-term elections (their exiled populist leader, Juan Perón, himself welcomed the prospect of a coup, and of a possible political deal).

Leading discussions on the structure of the future government, he put forth a blueprint prepared by his influential older brother, Álvaro Alsogaray, supporting the dissolution of democratic institutions, the enhancement of the judiciary as the guarantor of rights, and a more free market-oriented economic policy.

A key proposal was the creation of the post of Prime Minister, who would be given wide purview over policy, and to which the Alsogaray brothers intended that Álvaro be appointed by Onganía.

Disputes also arose with the Internal Affairs Minister, Dr. Guillermo Borda (who opposed any return to democratic rule), and with Alsogaray's successor as head of the important Campo de Mayo base, Major General Cándido López (who favored an early call for elections).

Amid a wave of political violence (Onganía removal was triggered by the execution of a former President, General Pedro Aramburu), a group belonging to the far-left ERP unsuccessfully attempted to kidnap Alsogaray on August 18, 1971.

[7] The younger Alsogaray was apprehended in February 1976 by counterinsurgency forces led by the Operativo Independencia Commander, General Antonio Domingo Bussi, and was executed.