The history of the Russian Orthodox Church in the Philippines began in the 20th century. In 1934, at the request of the Russian diaspora in Manila, Bishop Victor (Svyatin), responsible for China and Beijing, established a parish in honor of the Iveron Icon of the Mother of God. This parish operated until 1945, when the church was destroyed by shellfire.

In 1949, 5,500 Russian refugees from Shanghai, fleeing from Chinese communists, found temporary shelter on the uninhabited island of Tubabao. In April of the same year, Bishop John (Maximovich) of Shanghai arrived on the island, dedicating three months to caring for his flock. Two tent churches were quickly set up in the camp and a third in the building of a former American military church, provided by the Philippine authorities. The Russian community remained on Tubabao until the end of 1951. In 2013, a chapel named after the Holy Virgin, where Saint John served, was built on the site of the lost church.

In March 2014, representatives of the Independent Catholic Church of Mindanao, one of the denominations of the Independent Philippine Church, approached Patriarch Kirill of Moscow and All Russia with a request to join Orthodoxy. This decision was made after visits by Priest Kirill Shkarbulya, who brought humanitarian aid to those affected by Typhoon Yolanda in November 2013. As a result of missionary trips by Priests Georgy Maximov and Kirill Shkarbulya, new parishes of the Russian Orthodox Church appeared in Mindanao. Mass baptisms of Filipinos were conducted in the ocean, including the baptism of 239 people on August 21, 2015, in Ladol, including the Aglipayan community with two bishops and four priests who were received into Orthodoxy as laypeople.

Today, most Orthodox Filipinos, numbering about one and a half thousand, live on the island of Mindanao.

On February 10, 2016, the first meeting of the working group on the missionary activities of the Russian Orthodox Church in the Philippines took place at the Department of External Church Relations of the Moscow Patriarchate.

On December 28, 2018, the parishes of the Moscow Patriarchate in the Philippines became part of the Patriarchal Exarchate in Southeast Asia. On February 26, 2019, the Philippine-Vietnamese Diocese was established within the Exarchate.