Reconstruction efforts were done but were halted in 1688 because the place was declared unfit for habitation.
Construction resumed in 1696 under the supervision of Fr.
Francisco de Mondéjar and through the generosity of a pious person, Don Tomás de Endaya, and the stone church was completed in 1699.
The convent was also reconstructed alongside the church.
It was also during this time when the baroque altar was installed.
The new stone church was dedicated to then newly Blessed Pedro Bautista and to his companion martyrs who were beatified by Pope Urban VIII on September 14, 1627.
 They were canonized after almost a century and half on June 8, 1862 by Pope Pius IX.

Repairs were made in 1874 by a lay brother named Gabino Perez.

In 1895, the friars abandoned the place, and the following year at the time of the Cry of Balintawak, the Filipino revolutionary forces occupied the church.

In 1898, during the Philippine-American War, the American soldiers occupied the church.
Then, it was left idle until it was repaired in 1912.
In 1914, the church was blessed and a town fiesta was held to honor Saint Pedro Bautista.

Presumably, it survived bombardment of World War II due to the remoteness of its location at that time.
Reconstruction efforts were done but were halted in 1688 because the place was declared unfit for habitation. Construction resumed in 1696 under the supervision of Fr. Francisco de Mondéjar and through the generosity of a pious person, Don Tomás de Endaya, and the stone church was completed in 1699. The convent was also reconstructed alongside the church. It was also during this time when the baroque altar was installed. The new stone church was dedicated to then newly Blessed Pedro Bautista and to his companion martyrs who were beatified by Pope Urban VIII on September 14, 1627.  They were canonized after almost a century and half on June 8, 1862 by Pope Pius IX.
Repairs were made in 1874 by a lay brother named Gabino Perez.
In 1895, the friars abandoned the place, and the following year at the time of the Cry of Balintawak, the Filipino revolutionary forces occupied the church.
In 1898, during the Philippine-American War, the American soldiers occupied the church. Then, it was left idle until it was repaired in 1912. In 1914, the church was blessed and a town fiesta was held to honor Saint Pedro Bautista.
Presumably, it survived bombardment of World War II due to the remoteness of its location at that time.
Santuario de San Pedro Bautista