[6] Per the efforts of conquistador Martín de Goiti – who founded the City of Manila by uniting the dominions of Sulayman III of Namayan, Sabag, Rajah Ache Matanda of Maynila who was a vassal to the Sultan of Brunei, and Lakan Dula of Tondo who was a tributary to Ming dynasty China – the Diocese of Manila was established on February 6, 1579, through the papal bull Illius Fulti Præsidio by Pope Gregory XIII, encompassing all Spanish colonies in Asia as a suffragan of the Archdiocese of Mexico.

On August 14, 1595, Pope Clement VIII raised the diocese to the status of an archdiocese with Bishop Ignacio Santibáñez its first archbishop.

With the creation of these new dioceses, the territory of the archdiocese was reduced to the city of Manila and the adjoining civil provinces in proximity including Mindoro Island.

An example would be the Boxer Codex, whose earliest owner Lord Giles of Ilchester had inherited it from an ancestor who stole it from Manila during the British Occupation.

The opposition of the religious orders against an autonomous diocesan clergy independent of them lead to the martyrdom of Filipino diocesan priests Mariano Gomez, José Burgos, Jacinto Zamora collectively known as Gomburza who were wrongly implicated in the Cavite Mutiny, since the Spanish feared that because a priest, Miguel Hidalgo lead the Mexican war of independence against Spain, the same would happen in the Philippines.

[12] Furthermore the Governor General who was a Freemason, Rafael Izquierdo y Gutiérrez upon discovering the Cavite Mutiny was led by fellow Freemasons: Maximo Innocencio, Crisanto de los Reyes, and Enrique Paraiso; the Governor-General as per his Masonic vow to protect fellow brothers of the Craft, shifted the blame to Gomburza since they had inspired ethnic pride among Filipinos due to their campaign for reform.

[12] The Governor-General asked the Catholic hierarchy in the person of Archbishop of Manila Gregorio Meliton Martinez to have them declared as heretics and defrocked but he refused as he believed in Gomburza's innocence.

[12] This inspired the Jesuit educated and future National Hero Jose Rizal to form the La Liga Filipina, to ask for reforms from Spain and recognition of local clergy.

The combination of violent theft and arson done by the Japanese and indiscriminate carpet bombing by the Americans during the Battle of Manila (1945) led to the permanent loss of many of the ancient Gothic, Art-Deco, and Earthquake Baroque churches.

[15] In the aftermath of the war, in September 1942, Pope Pius XII declared Our Lady of Immaculate Conception as the Principal Patroness of the Philippines by virtue of the papal bull, Impositi Nobis, along with Pudentiana and Rose of Lima as secondary patrons.

[16] Due to the heavy damages resulting from World War II, the Manila Cathedral underwent major rebuilding from 1946 to 1958.

On December 11, 1948, the Apostolic Constitution Probe Noscitur further divided the Archdiocese of Manila by placing the northern part of the local church in the new Diocese of San Fernando.

Pope John Paul II declared the Manila Cathedral a minor basilica in 1981 through the motu proprio Quod ipsum, issued as a papal bull.

O'Doherty would lead the church during a period when Filipinos were petitioning for sovereignty from the United States and during the Japanese occupation of the Philippines during World War II.

After the departure of Cardinal-Archbishop Luis Antonio Tagle to assume the position as prefect of Congregation for the Evangelization of Peoples in February 9, 2020, Auxiliary Bishop Broderick Pabillo lead the archdiocese as apostolic administrator for 17 months during the COVID-19 pandemic, until Tagle's successor, then-Archbishop of Capiz José Fuerte Advíncula, took office in June 24, 2021.

The archbishop of Manila exercises authority in each member school and appoints a superintendent for the entire system to implement decisions and resolve issues.