After the Spanish retook New Granada, he was barred from the country and was exiled in Havana, where he continued his scientific studies and worked as a doctor.

His paternal grandfather, Don Luis Fernández Madrid was a knight of the Order of Calatrava and a member of the council to the King of Spain, and in the New World, served as oidor, or head judge, of the audiencias of Guatemala, and Mexico City.

He excelled in Congress and was known for his intellect, and speeches, and his literary works gave him great standing image among his colleagues.

[3] Congress elected Custodio García Rovira, Manuel Rodriguez Torices, and Manuel Restrepo to preside over the triumvirate, but since all of them were absent, congress named José María del Castillo y Rada, José Joaquín Camacho and Fernández, as interim presidents of the triumvirate.

The Spanish reconquest of the country was rapidly advancing under general Pablo Morillo from the royalist stronghold of Santa Marta.

On June 30, after the defeat of the Battle of Cuchilla del Tambo, the last battle of the Reconquista, Fernández and his wife are captured and taken prisoners in Chaparral while they were in search of the lands of the Andaquí Indians to seek refuge Then, captured and facing the real threat of facing the Judges of War and Purification, who would have sentenced him to death as was the fate of many very important figures during the Reconquista, he pleaded for forgiveness—a mistake he would later regret—and he implored for a meeting with general Morillo.

Because of his family's record of service to the king, and his lack of military action, his life was spared and sentenced to exile in Spain along with his wife, María Francisca Domínguez de la Roche, and his brother, Coronel Francisco Fernández Madrid.

José Fernández Madrid was named ambassador to the United Kingdom by Simón Bolívar on November 23, 1826[8] He was still in Paris when the government urged him to move to London as fast as possible.