Liliw, Laguna, was evangelized by Franciscan missionaries Juan de Plasencia and Diego de Oropesa in 1578 and initially served as a visita of the neighboring town of Nagcarlan. For almost three decades, the local residents had to travel to Nagcarlan for church services. In 1605, the people petitioned for their own parish, which was granted by Fr. Hernando de Morga, Superior of the Franciscans. The newly established parish was placed under the patronage of St. John the Baptist, with Fr. Miguel de San Lucas serving as the first parish priest. The construction of the first wooden church began in 1612 under Padre Kalenton, and by 1635, a concrete church was built under Fr. Antonio Kohaguit. The convent was completed in 1639 during Fr. Francisco Camera de Madre de Dios’s term.

Over the years, the church experienced significant damage, including from the 1880 earthquake and a fire in 1898, but it was promptly repaired. The church's architecture, particularly its use of red clay bricks for its walls, façade, and belfry, is a distinctive feature. Under various parish priests, including Fr. Philip B. Atienza, the church underwent beautification, including the installation of baroque-style retablos and a pulpit. During Fr. Atienza’s term, a parochial museum was also established to house surviving artifacts, preserving the rich history and culture of Liliw’s religious heritage.

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