In 1581, the first Jesuits from the Province of Mexico arrived in the Philippines. The mission was headed by Fr. Antonio Sedeño, the Superior. His companions were Fr. Alonso Sanchez and Brother Nicolas Gallardo. A fourth member, Scholastic Gaspar Suarez de Toledo, had died during the voyage from Acapulco. In 1585, the first novice was accepted, Juan Garcia Pacheco, a Spaniard. In 1591, mission stations were established in Balayan, Batangas, in Taytay, and in Antipolo, Rizal. In 1593, the first Jesuit mission stations were established in the Visayas in Tibauan, Panay. There, Fr. Pedro Chirino opened the first school of the Society of Jesus in the Philippines. It was a catechetical school for natives. Later the school was expanded with an elementary school both for Spanish and Filipino boys. The first Filipino in the Society of Jesus was a certain Martin Sancho or Sanchez. He was received into the Society in Rome. In 1601, he returned to the Philippines but died shortly thereafter of tuberculosis.
In June of 1595, Fr. General Claudio Acquaviva made the Philippine Mission into a Vice Province dependent on the Province of Mexico. Fr. Sedeño was its first Vice-Provincial. In September of the same year, the College of Manila was opened in the Jesuit compound in Intramuros on Calle Real (later Calle General Luna). The College offered courses in grammar, philosophy, theology, and canon law.
In the same year, residences of Jesuits were established in Cebu, in Leyte, and in Samar. Sometime later, residences were also built in Bohol and in Mindanao. The residential College of San Jose, attached to the College of Manila, opened on August 25, 1601. In 1605, just 24 years after the arrival of the first Jesuits, Fr. General Acquaviva made the Philippine Vice Province into an independent Province. By that time, the Province had 67 members who labored in one college of higher studies (the College of Manila), one residential seminary (San Jose), seven mission residences, and two mission stations.
In 1606, a novitiate was opened in Antipolo, but later the novices were transferred to the College of Manila. From 1622-1630, the novitiate was located in San Pedro, Makati, but in 1630, it again returned to the College of Manila. The novitiate building in Makati became a house of retreats and a villa house.
In 1656, 50 years after the establishment of the Province and 75 years after the founding of the Mission, the membership of the Province had risen to 108 (74 priests, 11 scholastics, and 23 coadjutor Brothers). There were five colleges, one novitiate, one Seminary-College, nine mission residences, and the spiritual administration of 73 towns. In these 75 years, 372 Jesuits had come to the Philippines from Europe and New Spain. 143 Jesuits had been admitted to and had persevered in the Society in the Philippines. Three had been received as priests, 23 as scholastics, and 117 as coadjutor brothers.
In 1668, the Philippine Province established a mission in the Marianas Islands. This mission later became a Vice Province dependent on the Philippine Province. By 1755, the Philippine Province had the spiritual administration of 80 parishes and missions in the Philippines and the Marianas, caring for a total population of 212,153 persons.
In 1768, the Jesuits were banished from the Philippines. On February 27, 1767, King Charles III of Spain had issued a decree banishing the Society of Jesus from Spain and the Spanish dominions. This decree reached Manila on May 17, 1768. Between 1769 and 1771, the Jesuits in the Philippines were transported to Spain and from there deported to Italy. The possessions of the Province were declared forfeit to the crown except the obras pias, which were maintained as ecclesiastical property. Among these was the College of San Jose, which continued to exist, first under the administration of the secular clergy and later under that of the Dominicans. The Jesuit parishes and missions were transferred to other religious orders.