As it traditionally happened among the Colleges of the Society in the Basque Country, they were founded or sponsored by Indian families. The college of San Francisco in Borja de Oñate followed this tradition. It was not the first Jesuit College established in this city. At the end of 16th century, the Araoz y Lazárraga family, native from Oñate, had paid the construction of a new college of the Society of Jesus with the fortune they got in Peru. It did not last so long. The founding resources that it had in 1510 were very few and the houses were it was established in 1551 counted on taxes. This caused the Order's transfer to Vergara. The Araoz y Lazárraga family was disappointed because its name and honor had decreased among the other residents. So, several years later, another member of the family, Martín de Araoz, a single and pious man located in Seville and with several businesses in Peru, attested on the 27th of March 1634 for the Society before travelling to Peru. The will stated that all his possessions had to be used for paying his debts, for the construction of a college of the Society in Oñate and the remaining part had to be given to his nephew Juan de Araoz y Lazárraga. In September of that same year, he died of an illness. His nephew Juan took charge of enforcing his will. It was very difficult for him because the resources given for the college, located in the called "Caja de difuntos" and controlled by the "oidores"* of Castile's Council, were stolen by the ones in charge of them. So, Juan de Araoz and the Society had to litigate to recover them. In 1634, 20.000 ducats and several worship pieces in gold and silver were used to open the college dedicated to San Francisco de Borja. The city of Oñate collaborated and was very committed to the opening of the school of basic education that started to be built in 1544. There are no more data related to this college's activity until 1767, when it became inoperative due to the Pragmatic Sanction published by Charles III (1759-1788).

*It is the Spanish name of the member judge of the Royal "Audiencias" and "Cancillerías", originally courts of the Kingdom of Castile, which became the highest organs of justice within the Spanish Empire.