The original church was built by Father Francisco Diez in the year 1710 in honor of the Blessed Virgin of Nativity. Church administration was transferred by Jesuit priests to Franciscan priests in 1768. It was consumed by fire in 1773 and rebuilt and enlarged under the direction of Father Roque de Osma in 1781. In 1853 Father Juan Navarette added a round bell tower. The design of the bridge was made in the shape of a cross by Father Antonio Sanchez in 1873. In 1887, the roof was replaced and replaced with a sink or metal by Father Arsenio Figueroa. In 1939, the administration of the church by the Franciscan priests was transferred to the first Filipino parish priest, Father Francisco Palomeras, who added a second floor to the bell tower. The third floor was built by Padre Potenciano Ortega in 1950.

It became the Borongan Cathedral in 1961. It underwent a major transformation and enlargement in 1962 by the Reverend Reverend Vicente P. Reyes, D.D., the first bishop of Borongan. Currently the circular bell tower is the only part of the old church that remains.