In that same year, the church obtained permission from the Superior Government to build the church using stone. Upon the order of San Pedro Bautista, head of the Franciscans, the church was rebuilt using bricks in 1600 but was later destroyed by the 1743 earthquake with the walls being left standing.
Sa utos ni Fray Pedro Bautista, na noon ay tagapamahala ng mga Pransiskano sa Pilipinas, itinayo ang simbahang bato noong 1600. Lubahang napinsala ito noong malakas na lindol ng 1743.