He studied theology at the Jesuit College of San Martin in Lima, and changed his given name to Bernardino upon joining the Franciscan order.
[3] These stances gained Cárdenas the favor of many of the Paraguayan settlers, who disliked the Jesuit missions as economic competitors among other complaints.
Governor Hinestrosa turned to the Jesuit armies of Indians to take control of the situation in Asunción; he compelled the local diocese to depose Cárdenas on the grounds his consecration had not been valid, and exiled him from Paraguay in November 1644.
Cárdenas left for Corrientes, where he continued to engage in a war of letters and propaganda against Hinestrosa with the support of his fellow Franciscans.
In 1647, he met incoming Governor of Paraguay Diego de Escobar y Osorio, and convinced him to allow his return to the province.
[3] Immediately upon the proclamation of the order, a mob broke into the Jesuit college of Asunción, sent the friars into the streets, and looted the building of its valuables.
Cárdenas was imprisoned by León y Zárate, and the citizens of Asunción suffered what to them was the humiliating spectacle of an occupying army of Indians.
Cárdenas was reprimanded for accepting the result of the election based on the old decree and for expelling the Jesuits without royal permission, but received no further punishment.