[2] Alvares was ordained a Roman Catholic priest in 1862 or 1864 by Bishop Walter Steins SJ, Vicar Apostolic in Bombay.

When, under Pope Pius IX and Pope Leo XIII, the hierarchy in British India was formally reorganised independently of Portugal but with Portuguese consent, a group of pro-Padroado Goan Catholics in Bombay united under the leadership of Dr. Pedro Manoel Lisboa Pinto and Alvares as the Society for the Defense of the Royal Patronage and agitated against the Holy See, the British India government and the Portuguese government in opposition to these changes.

Alvares had lived in Colombo, Sri Lanka, for a significant time which is why he ended up having a Cathedral at this location.

Alvares had also lived in the twin villages of Brahmavar and Kalianpur, Karnataka, which is now where The Evangelistic Association of the East has many churches and has been doing extensive mission work to support the descendants of Alvares converts from his initial missions in these areas and also to continue his missionary work.

[3][need quotation to verify] He ordained Joseph Kanianthra, Lukose Kannamcote and David Kunnamkulam at Brahmawar on 15 October 1911.

[5]: 6  The Padroado was the privilege of patronage extended to Portugal which granted the right of designating candidates for episcopal and other offices and benefices in Africa and the East Indies; in addition, it was an exchange of a portion of ecclesiastical revenues for missionaries and endowments to religious establishments in those territories.

In time it was seen by the Holy See as an obstacle to missions: the Portuguese government failed to observe the conditions of the agreement; disagreed about the extent of the patronage by claiming the agreement was restricted by Pope Alexander VI's Bulls of Donation and Treaty of Tordesillas while Rome maintained the agreement was restricted to conquered countries; and, contested papal appointments of missionary bishops or vicars apostolic made without its consent, in countries which were never subject to its dominion.

[6] As part of the transition, churches served by Goan Catholic priests remained under the jurisdiction of the Patriarch of the East Indies until 1843.

In British Ceylon, it ended in 1887 with the appearance of a papal decree that placed all Catholics in the country under the exclusive jurisdiction of the bishops of the island.

Alvares and Dr. Pedro Manoel Lisboa Pinto founded in Goa, Portuguese India, an association for the defence of the Padroado.

Then, according to G. Bartas, in Échos d'Orient, they complained that the new diocese and vicariates were headed, almost exclusively, by European prelates and missionaries, and petitioned the Holy See for the creation of a purely native hierarchy.

[b] Aiya wrote that Alvares, an educated man and the editor of a Catholic journal, was a priest in the Metropolitan Archdiocese of Goa.

[7][12]: 6 Michael Roberts, in Sri Lanka Journal of Social Science, describes three groups within early nationalism in British Ceylon.

The most prominent group, "ultra-moderate constitutionalists", with culture and value system significantly westernised, whose main goal was greater participation in government; the second group, "mild-radicals", represented by leaders like Pinto, was a labour movement with political radicalism and interest in more radical trade unions; the third group, "religio-cultural revitalists", traditional values Sinhalese Buddhists "which expressed militant objection to changes produced by Western penetration."

Smit observed that past "experiences had made ... the IBC cautious, which in his opinion was a reason for the failure of contacts with groups in ... Ceylon ... and other countries to develop into relationships of full communion.

[17] Bartas did not recount the significance of Alvares' ideology,[e] he only noted that the schism, around 1902, intended to convert corporately, to eastern orthodoxy.

He and his parishioners asked the Holy Synod of the Church of Greece, in Athens, to accept them under its jurisdiction and to send them an officiating priest preaching in Latin and English.

Bartas wrote: A Greek Orthodox priest, delegated by the Holy Synod in Athens, to celebrate the Latin Mass and deliver the English sermons, in an independent Catholic Church of Ceylon in the cathedral of the priest who became Archbishop of Goa Indo-Ceylon by the grace of a Jacobite bishop of Malabar; that is the answer to a purely indigenous hierarchy, that ... Pinto and Alvarez demanded so loudly at the beginning of their schism!

He was arrested,[further explanation needed] stripped of his episcopal vestments and taken through the street in his underwear to the police lock-up and placed into a filthy prison cell without a bed or chair.

After a few days, he was arrested again and charged with the offence of high treason,[further explanation needed] but again the Justice found him innocent.

], placed in a lead box and reburied, under a marble slab with the inscription "Em Memoria De Padre Antonio Francisco Xavier Alvares, Diue [sic] Foi Mui Humanitario Missionario E Um Grade [sic] Patriota" (In memory of priest Antonio Francisco Xavier Alvares, who was very humanitarian missionary and a great patriot) and the largest cross in the cemetery.

In 1967, John Geevarghese, the first resident Vicar of St. Mary's Orthodox Church, Goa, rediscovered the forgotten grave of Alvares, and brought Metropolitan Mathews Mar Athanasios of the Outside Kerala Diocese to Goa to conduct services befitting an Orthodox bishop at the burial site.

His dukrono, a memorial feast, is celebrated at St. Mary's Orthodox Syrian church in Ribandar on 23 September every year.