Protestantism developed in the Philippines after the Spanish–American War when the United States acquired the Philippines from the Spanish with the 1898 Treaty of Paris. Under American rule, the Catholic Church was disestablished as the state religion, giving Protestant missionaries more opportunities to enter the islands. In addition, there was a backlash against the Hispanic Catholicism and a greater acceptance of Protestantism represented by the Americans. The dominance of the Catholic Church in all aspects of life in Spanish Philippines and Protestant anti-Catholic animosity were prominent reasons for the start of Protestant missionary activity. In 1901 the Evangelical Union was established in the Philippines to co-ordinate activities amongst the Protestant denominations and lay the foundations for an indigenous religious movement.
The first Protestant service held in the Philippines was on Sunday, August 28, 1898. Chaplain George Stull, a member of The Methodist Episcopal Church, came with the occupying forces. Although his primary duty was to minister to the soldiers, he recorded in his diary that that first service, held in an old Spanish dungeon facing Manila Bay, was attended not only by his own men but by some Filipinos as well. He commented on this service:
"That the power of God will use this day to make a good Catholic better, any weak American stronger, any backslider ashamed, and the gloomy old dungeon the beginning of wonderful things in these Islands, is my prayer."
After the defeat of the Spanish in the Battle of Manila Bay by the U.S. Navy's Asiatic Squadron, Presbyterian, Baptist and Methodist leaders met in New York to discuss how to bring Protestants to the Philippines in 1898. The result was a comity agreement of the missionary enterprises, dividing up places of ministry to avoid future conflicts among themselves and their converts. Only one Protestant church would be started in each area. The comity agreement, which led to the territorial division of the Philippines, was one of the accomplishments of mission enterprises in the Philippines. The meeting was followed by another gathering in 1901 by the early missionaries in Manila to further discuss the comity agreement with three specific major agenda items:"to organize the Evangelical Union,"
"choose a common name for Protestant churches," and
"delineate the geographical work allotments for each church."
From 1898 to 1930 there were different Protestant missions agencies joining the comity agreement, namely:Methodists (1898, most of lowland Luzon and north of Manila);
Presbyterians (1899, Bicol, Southern Tagalog area and some parts of Central and Western Visayas);
Baptists (1900, Western Visayas);
United Brethren (1901, Mountain Province and La Union);
Disciples of Christ (1901, Ilocos, Abra, and Tagalog towns);
Congregationalists (1902, Mindanao except for the western end); and
Christian and Missionary Alliance (1902, Western Mindanao and Sulu Archipelago).
Brethren (Kapatirang Kristiano) linked to Plymouth Brethren, was established in the 1930s in San Juan, Metro Manila by a missionary named Cyril H. Brooks. They planted numerous chapels in the Philippines with majority in Bulacan, Pampanga and Rizal Province.
Manila was opened to all denominations and mission agencies. The Seventh-day Adventist Church and the Episcopal Church in the Philippines did not join because they wanted to go to all parts of the archipelago. American Protestant Missions (APM) emphasized institutional ministry and medical missions in their evangelistic and missions endeavors.
For a short time the comity agreement worked well, until the situation grew more intricate and splits occurred. The Methodists split in 1909 when Nicolas Zamora the Iglesia Evangelica Metodista en las Islas Filipinas (IEMELIF). This shattered the agreement. Thus, the IEMELIF became the first indigenous evangelical denomination, an all-Filipino-supported church at that time, with Methodist Ilocanos from Northern Luzon moved into the areas of the United Church of Christ in the Philippines in Mindanao. Baptist Ilonggos migrated from Iloilo to Central Cotabato, traditionally Christian and Missionary Alliance territory. As this kind of movement increased, the sharp boundaries between the different comity areas became obscured.
Divisions came with growth and expansion, and personality clashes, racial tensions, the dynamics of nationalism, cultural differences, power struggles and other non-theological factors contributed to the schisms. In the 1920s the fundamental-modernist controversy in the USA affected the Philippines, causing further division. By 1921, some nineteen independent denominations were registered with the Security and Exchange Commission (SEC) and important splits occurred among the Methodists, Baptists, Presbyterians and Disciples of Christ. Several small denominations, some of them entirely under national leadership, emerged.
Unity of the churches was still a goal. In 1929, the United Brethren, Presbyterian and Congregational Churches formed the United Evangelical Church in the Philippines. In 1932, six of the smaller indigenous denominations of Presbyterian and Methodist backgrounds formed the Iglesia Evangelica Unida de Cristo, or now more commonly known as the Unida Christian Church. The assembly of these indigenous denominations was called by Don Toribio Teodoro, owner of the Ang Tibay shoes. The National Christian Council was founded in 1929 as a successor of the Evangelical Union. This was followed in 1938 by the organization of the Philippine Federation of Evangelical Churches. With the coming of World War II, the United Evangelical Church underwent severe trying circumstances when the mission agencies were completely cut off from the USA. American missionaries were incarcerated and mission funds were unexpectedly discontinued.
To deal with the diverse Protestant groups, the Japanese during their occupation of the Philippines during Second World War pressed for the formation of the Evangelical Church of the Philippines which combined thirteen denominations. However, most of the larger denominations such as Methodist, Episcopal, Unida and other independent churches refused to join. After the war, the Evangelical Church of the Philippines further fragmented, but the Disciples of Christ, the United Brethren, the Iglesia Evangelica Unida de Cristo, the Evangelica Nacional, some individual congregations of the IEMELIF, the Philippine Methodist and the Presbyterian Churches remained intact. Several churches united to form the United Church of Christ in the Philippines in 1948. In 1949 the United Evangelical Church, the Philippine Federation of Evangelical Churches, and the Iglesia Evangelica Unida de Cristo formed the Philippine Federation of Christian Churches, now called the National Council of Churches in the Philippines. Today, Protestant and evangelical churches and denominations are grouped into major councils of churches: The National Council of Churches in the Philippines (NCCP) for mainline Protestant churches and the Philippine Council of Evangelical Churches (PCEC) for evangelical churches, organized in 1964.
Several independent church organizations emerged in the 1970s and mid-1980s, such as the Jesus Is Lord Church, the Greenhills Christian Fellowship founded in 1978 by the Conservative Baptists, the Bread of Life Ministries International founded in 1982, and the Christ's Commission Fellowship and Victory Christian Fellowship both established in 1984. These churches used mass media to spread evangelical Christianity in the country and to establish more non-denominational, Pentecostal, and charismatic churches. These churches grew up rapidly and are considered one of the major Protestant megachurches in the Philippines.
A major factor in the development of Philippine Protestantism is the explicit expression of religious freedom found in Section 5, Article III ("Bill of Rights) of the 1987 Constitution, separating church and state. The concept and its English phrasing has been present in every national charter since the 1935 Constitution promulgated by the Commonwealth government. The Philippine Youth Movement founded in 1926 boosted the move to develop the indigenous Protestant church nationwide.
A theme in the development of Protestantism in the Philippines is the tension between the religion and nationalism. After an initial period of resentment toward American missionaries, Filipinos gradually accepted Protestantism. During the 1920s and '30s, American Methodist missionaries openly supported Filipino independence from the United States.
Protestant missionaries founded many schools and universities in the Philippines. Some of which are founded by early American Protestant missionaries. Most notable of these is Silliman University, the first Protestant school in the country and the first university founded by Americans in Asia. Silliman is followed by the Central Philippine University, its sister institution, and other institutions of higher learning such as Trinity University of Asia, West Negros University, Filamer Christian University, the Philippine Christian University and the Adventist University of the Philippines.
Some are members of the National Council of Churches in the Philippines, Philippine Council of Evangelical Churches, Philippines for Jesus Movement, Christian Conference of Asia, World Methodist Council and the World Council of Churches.