The church itself is a testament of a religious controversy rooting back from Marikina's early history wherein both the Jesuits and Augustinians fought over the ecclesiastical control of the area.

On March 10, 1687, Governor Gabriel Cruz Elasque ordered the transfer of Marikina to the oversight of the Augustinians and merged with the ministry of San Mateo.

He instructed Don Juan Pimentel, the Mayor of Tondo, to vacate and demolish the visita of Jesús de la Peña as the Marikina River would flood the site during the rainy season.

The visita could not accommodate the growing congregation, forcing the Augustinian friars to transfer operations across the Marikina to higher ground, where the much larger, present structure was built.

By 1957, OLA church was restored and refurbished by Father Silvestre dela Cruz of Archdiocese of Manila with the help from various religious and civic organisations.

[citation needed] Meanwhile, then Bishop of Antipolo Crisostomo Yalung honored the Patrona with an Episcopal Coronation to remember the 100th Anniversary of the venerated image.