In 1668, Fray Nicolas Santiago began building the stone church that still stands today. At 180 feet by 38 feet, it was one of the first towns in the country to have its parish and municipal halls adjacent or housed within same vicinity.

In 1731, Father Juan Francisco de San Antonio began construction of the present convent, then succeeded by Fray Miguel de San Bernardo and finished under the administration of Jose Sellez. In 1784, Fray José Cantos rebuilt the wooden portions of the church with hewn stones. The Franciscans noted it as being one of their best convents.

The bell tower was built by Father Francisco Gascueña in 1800, and is one of only two such structures with a large arch bridge connecting the church to its base. The tower had five bells, including the largest one named Maria Conception in 1878. The other bell was also ordered by year 1881—San Francisco in honor of the town’s patron saint and namesake.

The people of the parish loved Father Gascueña so much that when he died on November 1831, they buried him beneath the main altar as a gesture of respect. Throughout his thirty-one years of service to both poor men and women, he had been known for his kindness through charity.

From 1832 to 1850, Father Balbino de Consuerga completely renovated the church’s wooden parts. He also added a large hall and sacristy. In 1851, Father Benito de Madridejos repaired damages and commissioned new altar pieces in order to restore its former glory.

The American army used the church and its convent as a headquarters after seizing it from Filipino revolutionaries in May 1899. During that time, many of the building’s possessions were believed destroyed or looted by U.S soldiers.

The Church survived the destruction that befell other churches in Manila during World War II; however, it was destroyed by a massive fire known as “The Great Fire of Meycauayan” in 1949.

The fire destroyed not only the church’s records and vestments, but also its statues and old memorabilia—even its retablo. Only a few items escaped destruction: one of them is the tabernacle, which was moved to safety before flames began spreading through that part of the complex; now it can be seen in display at parish museum. After its destruction, the people of the town helped to rebuild it.

The church recently had its interior walls restored and sanctuary renovated, recreating the neoclassic altarpiece of Father Benito Madridejos.

It is worth noting that, in the early years of the town’s settlement, The Franciscans who came to Meycauayan brought with them a wooden cross—similar to Magellan’s Cross. Since then this relic has been known as “The Cross of Sitio Torril”—the town’s oldest-known religious artifact. The relic is brought out for public veneration during the October 4th celebration every year.