The "Society of the Missionaries of St. Francis Xavier", commonly known as the "Society of Pilar", was started by Fr. Bento Martins on 26th September, 1887. Fr. Bento then was a humble diocesan priest in a nondescript village of Agonda in Goa. But being afire with the zeal of spreading the Gospel to the new places brought under the erstwhile Portuguese Rule, he formed a group of like-minded priests and named the Society after the great Jesuit Missionary, Francis Xavier.

In 1891, the then Patriarch of Goa, Dom Antonio S. Valente gifted to the fledging Society an abandoned monastery perched on a hillock which eventually became the mother house of the Society. The hillock with the locality is called Pilar and is situated 12 kms southeast of Panjim, the capital of Goa. Thus the Fathers came to be known as "Pilar Fathers", after the monastery that had as its patroness Our Lady of Pilar, a devotion to Mary prevailing in Saragosa, Spain that was brought to Goa by the Franciscan monks. The Society adopted Our Lady of Pilar as its patroness. Hence it is also called the Society of Pilar or the Pilar Fathers. Though a small batch, the Society was very vibrant in missionary activity catechizing in various talukas in and outside Goa. The Society also had renowned preachers and Pilar became a centre for retreats and renewal. One of the members of this Society, Fr. Agnelo de Souza, was well-known for his heroic sanctity. Soon after his death on 20th November, 1927, his fame spread far and wide. People flock to his tomb to pay their respects. In 1987, the Holy Father declared Fr. Agnelo, Venerable and the process of beatification is still in progress in Rome.

After a couple of decades of hectic missionary activity the Society of Pilar went through hard times due to the ban on religious societies by the Portuguese authorities and also the death of its founder Fr. Bento who died of malaria at a very young age of 49. The older members passed away, some left the Society, and no new members were joining. It numbers began dwindling and the Society was on the verge of extinction. Eventually in 1939, there was just one lone surviving member, Fr. Remedios Gomes who kept the flame burning. Providence came to the Society’s rescue. It did not die. It was at this juncture in 1939, with divine intervention the Society received a spurt of new life when five young and enthusiastic diocesan priests among whom were the dynamic Fr. Conceicao Rodrigues and Fr. Francisco Sequeira. They too were inspired by the zeal of Francis Xavier, and determined by a pledge they made to the saint, strove to give new life to the dying society and thus revived and reorganized the old Society introducing the rule of common life with private vows of poverty, chastity and obedience.

The Second Founders of the Society as they subsequently came to be called gave a new thrust to the missionary activity making it the principal aim of the Society, and widened its scope to embrace the whole of India. A thing that was uppermost in their minds was that the Society should have its own seminary to ensure its continuance and growth. That became a reality and 12 years later this Seminary presented its first fruits of three priests. Since then the Society has been flourishing.

Since the Society founded by Fr. Bento Martins was re-organized by the eight pioneers of the re-organization namely, Fr. Menino Conceicao Rodrigues, Fr. Francisco Jasso Sequeira, Fr. Baltazar Remedios do Rosario Gomes, Fr. Manuel Jose Barreto, Fr. Joseph Albuquerque, Fr. Theodolindo Cabral, Bro. Peter Mascarenhas and Bro. Paixao Lacerda, the foundation and the re-organization form two distinct moments in the life of the Society of the Missionaries of St. Francis Xavier – the latter transforming the former, this being a unique phenomenon rarely witnessed in the history of religious institutes and societies of apostolic life. The re-organized Society of 1939 is canonically, the continuation of the same Society founded in 1887.