Like the other churches in the Philippine islands, the Church of Tumauini was originally made of light materials. In 1707, it was built by Fray Francisco Nuñez, OP, and dedicated to the patron saint, San Matias. Tumauini was separated from Cabagan and became a regular parish on May 7, 1751.
In 1783, the church of stone with a unique cylindrical bell tower was constructed by Father Domingo Forto. It was completed in 1805. The four-layer, cake-like bell tower is the only of its kind in the Philippines.
The Royal Decree of May 1, 1856 authorized the creation of the Province of Isabela in honor of Queen Isabella II of Spain. Tumauini became the capital of Isabela for sometime.
The church was partly damaged during the World War II but was repaired into its original form by the faithfuls of Tumauini.
By virtue of Presidential Decree No. 260, issued by President Ferdinand E. Marcos on August 1, 1973, as amended by Executive Order No. 375 dated January 14, 1974, and Executive Order No. 1505 dated June 11, 1978, the St. Matthias Church was declared as a national historical landmark on February 24, 1989.
On July 31, 2001, the St. Matthias Church was one of the Philippine colonial churches declared by the National Museum as a national cultural treasure. The National Commission for Culture and the Arts had identified and selected it as one of 26 Spanish Colonial Era churches to be under its conservation program.
On May 16, 2006,St. Matthias Church was one of the five Philippine Baroque churches submitted by the NCCA to the the Secretariat of the United Nations Educational Scientific and Cultural Organization (UNESCO) and the World Heritage Centre. It is now included in the Tentative List of the World Heritage Sites.