At the age of 15 he received a scholarship to study theology in the Colegio de San Bartolomé y Santiago in Granada.
He collected paintings by Velázquez, Rubens, Titian, etc., and his library contained the most modern works on all branches of knowledge.
Sailing to Cuba in the spring of 1776 for his consecration, he was accompanied by much of his family and friends, including his nephew Manuel Torres.
He reorganized the Colegio de San Pedro, which had fallen on hard times since the expulsion of the Jesuits in 1767.
In 1777 he was named archbishop of Santa Fé de Bogotá in the colonial Viceroyalty of New Granada by King Charles III, and confirmed by the pope.
For his services, King Charles subsequently made him a member of the Order of Carlos III and viceroy of New Granada.
To institute these reforms, the Crown sent Juan Francisco Gutiérrez de Piñeres to the colony in 1777, with the title of visitador (inspector).
Viceroy Manuel Antonio Flórez had left the capital for Cartagena to defend against an expected attack there by the British.
Viceroy Manuel Antonio Flórez resigned on 26 November 1781 and was replaced by Juan de Torrezar Díaz Pimienta, governor of Cartagena.
A sealed letter opened after his death directed that the new interim Viceroy of New Granada should be Archbishop Caballero y Góngora.
He stimulated the economy, industry and the arts, and greatly assisted the Royal Botanical Expedition of 1783, under José Celestino Mutis.
In October 1784 he went to Cartagena to settle the Indian population in towns, and to suppress an Indigenous rebellion in Darién and promote colonization there.