It was first established as a mission station by the Jesuits in 1596 under the advocacy of Saint Ignatius of Loyola.

[notes 1] The first church made of nipa and hardwood was dedicated to Saint Ignatius of Loyola.

[2] A new church made of stone, along with a fortress, was built to protect the town from Moro invasion in the 1600s.

Father Juan Isandi,[notes 2] last Jesuit priest to Capul, died during the Moro attacks in 1768.

Father Valero designed the church with a cross-shaped wall made of stone, similar to Intramuros.