During the Victorian era, under the influence of Bishop Jean-Baptiste Lamy, the church was remodeled with Gothic Revival elements, including bell towers, a new pitched roof, and interior decorations, to give it a more European appearance.

[6]: 116 The governor, Fernando de la Concha, called the church collapse a disgrace and ordered everyone in the surrounding area to help in constructing a replacement as soon as possible.

In 1817, the administration of San Felipe de Neri was transferred to the Diocese of Durango,[5] as the Franciscans had outlived their intended missionary role and were draining the province's funds by continuing to draw a sizable government subsidy.

[6]: 117–120 Under the influence of Bishop (later Archbishop) Jean-Baptiste Lamy during the 1850s and 60s, the church was remodeled to give it a more Anglo appearance, with a pitched roof, vernacular Gothic Revival spires, and a new altar and pulpit painted to look like marble.

San Felipe de Neri is cruciform in plan with thick adobe walls, wooden vigas, and carved corbels dating to the original 18th century construction.

The exterior features twin bell towers, added around 1861, which show a vernacular adaptation of the Gothic Revival style using local materials.

Interior details from the same period include the altar and pulpit, which are constructed from wood painted to look like marble, tongue-and-groove wainscoting, and wooden cabinetry in the sacristy.

Rebuilt around 1890 by the Jesuits, the present rectory is a rectangular, two-story building of stuccoed brick with a wide portico, cross-gabled roof, and widow's walk.

This proved challenging for the local builders and required an Italian mason to be brought from Santa Fe to lay the stone foundation.