During this year hacienda in Looc, straddling the boundaries of Batangas and Cavite, bequeathed to the Jesuits’ Colegio de Manila, was added to Maragondon's jurisdiction.

The government ordered its demolition for fear that the Dutch, who were at war with Spain, would use it and other churches near Manila for fortification.

The orders were apparently implemented because on May 16, 1650, a license was given to the Jesuits to build a house and church of wood in Maragondon to replace the one that had been demolished.

After 1860 the Recollect added windows with colored glass panes, and set these in a wooded frame decorated with a quail on a plate, the attribute of San Nicolas de Tolentino.

”[1] The secular priest de los Reyes also did some repairs probably during the convocation of the second Vatican Council which was commemorated in the Philippines with a jubilee year.

In contrast to the simplicity of its façade is the ornate door, divided into boxes, with floral designs of different shapes and ships and castles carved on it.

Also polychromed in red, blue, gold, and green, is an octagonal pulpit, located at the right side of the church.