He studied law at Córdoba University and obtained his doctorate at the Real Universidad de San Felipe in Santiago.

By the end of 1813, Juan Larrea (a rich and influential friend of Alvear and of British commerce) replace Álvarez Jonte, who was named to lead the commission investigating the military defeats at Vilcapugio and Ayohuma.

Álvarez Jonte travelled to Tucumán to start the investigations and legal proceedings, but later he declined to judge general Belgrano.

Álvarez Jonte then returned to Buenos Aires, where he served as general war comptroller, and worked in this post during the brief government of Alvear.

There he joined the local Lautaro Lodge and dedicated himself to the formation of a navy squadron for Chile, recently liberated from Spain by San Martín, supporting the latter's plans to attack the Viceroyalty of Peru by sea.

He arrived in Chile with Admiral Thomas Cochrane in November 1818, with the navy's ships intended to move the Army of the Andes to Peru.