Mission San José y San Miguel de Aguayo was founded by Franciscan missionary Father Antonio Margil de Jesús in 1720. In 1768, construction of the existing church began.
The church’s façade and Rose Window are considered the finest examples of Spanish colonial ornamentation in the U.S. and the cupola and façade were heavily
ornamented with colorful geometrical designs. The church was richly embellished with carving and statuary.

As the center for religious and social development, it was the place for the Mass, an assembly hall, and a building for baptisms, weddings, and funerals.
The stone friary, started in the 1740s, was probably constructed as a series of units built eastward from the church wall and, with its gardens, had a circumference of about 416 feet.
Other structures included a granary, a carpentry shop, a blacksmith shop with a dwelling for the smith and his family, and a weaving workshop.

The church holds a bilingual Mariachi Mass every Sunday at 12:30 pm.
A UNESCO World Heritage Site