Its revolutionary nationalist schism from the Roman Catholic Church was proclaimed during the American colonial period in 1902, following the end of the Philippine–American War, by members of the country's first labor union federation, the Unión Obrera Democrática Filipina, as a response to the pronounced mistreatment of Filipinos by Spanish priests and partly influenced by the unjust executions of José Rizal and Filipino priests and prominent secularization movement figures Mariano Gomez, José Burgos, and Jacinto Zamora,[22][23] during earlier Spanish colonial rule when Roman Catholicism was the state religion in the country.

Originally professing to Trinitarianism, the Philippine Independent Church unofficially shifted to a Unitarian theological doctrine during its earliest years but has reverted to Trinitarinism since 1947 to present.

[32][33] During the earlier Philippine Revolution, Aglipay and his former college schoolmate and fellow anti-friar Isabelo de los Reyes (also known as Don Belong), an ilustrado author, journalist, and labour activist who was in exile in Spain at the time, acted to reform the Filipino Catholic clergy which was then dominated and controlled by Spanish friars ("frailocracy") as Roman Catholicism was the state religion at the time of the Spanish colonial period in the Philippines.

[34][35] Then-President Emilio Aguinaldo persuaded Aglipay to head the native Filipino clergy by appointing him military vicar general of the Philippine Revolution in 1898, wishing to overthrow the spiritual power of the Spanish friar-bishops.

[36][8] Isabelo de los Reyes was the chief initiator of the separation and suggested in absentia that Gregorio Aglipay, knowing that he was influential with the Filipino clergy,[41][42] should be the founding head, or Obispo Maximo (Supreme Bishop), of the church which was unanimously agreed by the members present in the proclamation.

[48][32][49] On October 28, 1903, the IFI adopted the Doctrina y Reglas Constitucionales (DRC), which replaced the Fundamental Epistles as the doctrinal foundation and governing rules of the Church, with slight revisions in 1918 and 1940.

Although not a Mason himself, de los Reyes — who created a distinct doctrine, liturgy, and organization for the Philippine Independent Church — drew on aspects of their theology and worship, which was then approved formally by Aglipay.

[38][59][60] Before being elected, Fonacier initially committed to steer the IFI back to Trinitarism, however during his tenure, his theological and doctrinal stance was evidently still leaning towards his predecessor's Unitarian beliefs.

On January 21, 1946, Fonacier was ousted from his position after a unanimous decree by the church's Supreme Council of Bishops due to controversies regarding certain decisions he imposed, which were deemed allegedly unconstitutional.

[62] Before his death, first supreme bishop Gregorio Aglipay had previously sought bestowal of apostolic succession from other denominations abroad for years, but failed due to his Unitarian theological beliefs and past revolutionary activities.

[7][68][69] Fonacier and Jamias's group, on the other hand, remained Unitarian, and eventually became known as the "Independent Church of Filipino Christians" (ICFC) which would later become a member of the International Association for Religious Freedom (IARF).

He was buried at the María Clara Christ Church on October 17 after having lain in state for one full week at the Iglesia Filipina Independiente National Cathedral which he had built in Taft Avenue, Manila.

The said reunification attempt failed when the majority of the ICFC clergy, including Fonacier's legal counsel and son-in-law Rizalino R. Pablo, did not conform to the agreement of reconciliation due to their firm adherence to their Unitarian beliefs.

[14][73][74][15] In the latter half of the 1990s, Ga voluntarily reconciled with the IFI, which led to the signing of a memorandum of agreement that paved the way for the mass return of a fair number of congregation and clergy in the Ilocos Norte and Cotabato areas.

[29] Ga's return to the IFI resulted in another breakaway group from the ICFI/PICC that was established in 1995 under the name "Aglipayan Christian Church Inc. (Legion of Mary)", which is based in Davao City.

Some of the members of the church, like the founders de los Reyes and Aglipay, are political activists, often involved in progressive groups and advocating nationalism, anti-imperialism, social justice, democracy, labor rights, as well as opposing extrajudicial killings.

They have often been victims of enforced disappearances and been branded as leftists by the government for being aligned with progressive groups, specifically after Alberto Ramento, the ninth supreme bishop, was killed in 2006 for being an anti-government critic.

Aglipayans maintain that the belief in the real presence does not imply a claim to know how Jesus Christ is present in the Eucharistic species (the consecrated bread and wine) and is left to mystery.

Subsequently, the clerical vestment designs inspired by the Philippine Flag colors and symbols are still practiced up to this day by the IFI in honor to its nationalist and revolutionary heritage.

The Iglesia Filipina Independiente views their history of liberation from the Roman Catholic Church during the colonial era in the Philippines as comparable to that of the story of Exodus which can be found in the religious book of the same name in the Bible.

The vow of poverty is not stated in the Constitution and Canons, although priests are strictly mandated to always put their ministry on top priority wherein it should not be compromised when permitted to have an occupation outside the church.

On May 5, 2019, Emelyn Dacuycuy of the Diocese of Batac became the first woman to be consecrated bishop in the Iglesia Filipina Independiente, further asserting their belief in women's inclusion and breaking the tradition of patriarchy in the clergy.

During Lenten season, a group of WOPIC members in certain dioceses called nobisyas (literally translated to novice in English) render 40-day church services as their pamamanata (act of penance) and wear veil as "an honorable way to imitate Mary, mother of Jesus", same thing with the seven women "dolorosas".

An ordained who had joined an electoral contest, being an official candidate and lost, may be admitted again to the ministry and apply for a reinstatement to the Supreme Council of Bishops (subject for approval) as long as he/she completes a one-year refresher course in one of the IFI's seminaries.

On the other hand, an ordained who won an election may also be admitted again to the ministry and apply for a reinstatement to the Supreme Council of Bishops, after he/she officially ends his/her political tenure and must not concurrently hold a government position, as long as he/she also completes a one-year refresher course.

[29] During the early days of the schism particularly in September 1903, the church, led by Aglipay together with a number of bishops, canonized José Rizal and the Gomburza priests in a closed-door conference.

[100][101] Aglipayan bishops joined public demonstrations in support of the Reproductive Health Bill, a legislation advocating for contraception and sex education to reduce the rate of abortion and control rapid population growth that the Roman Catholic Church and several other Christian denominations objected to on moral grounds.

The statement – dubbed "Our Common Humanity, Our Shared Dignity" – stresses the church's position that it "must openly embrace God's people of all sexes, sexual orientations, gender identities, and expressions (SSOGIE)."

[107] According to the officials, the IFI's stance on the controversial subject stems from its teachings that emphasize the "people's rights for freedom, dignity, and integrity, which also means encouraging the society to be responsive to the realities of time and to recognize that there have been unions that were wrong".

[7][69][68][30][77][8][98] The Iglesia Filipina Independiente has been in an ongoing interreligious dialogue with the Roman Catholic Church since the latter part of the 20th century and their "joint statements" were eventually made official in 2021.