The church was founded in 1706 by Fray Manuel Moreno, one of the original settlers of Albuquerque. It was first dedicated to Saint Francis Xavier, but the Viceroy changed the patron saint to Saint Philip Neri in July 1706 to honor King Philip V.
The first church fell down in the winter of 1792 to 1793. The governor called the collapse a disgrace and ordered everyone nearby to help build a new one. Construction on the second church began in 1793.
Under Bishop Jean-Baptiste Lamy in the Victorian era, the church was remodeled with Gothic Revival bell towers and a pitched roof. It is the only building in Old Town proven to date to the Spanish colonial period, and it has been in use for over 200 years.