Spanish settlers first came to the Santa Cruz area around 1598 under the protection and religious charge of the San Gabriel mission in Ohkay Owingeh Pueblo. This settlement lasted until 1680 when a massive uprising of the Native Americans, led by the Okhay Owingeh medicine man, Pope, was successful in driving the Spanish from New Mexico.
When the Spanish re-colonized New Mexico they quickly moved to regain control of the middle Rio Grande valley. In 1695 the town of "Villa Nueva de Santa Cruz de los Españoles Mejicanos de Rey Nuestro Señor Carlos Segundo" became the second town established by the Spanish (Santa Fe being the first).
The present church of Santa Cruz de la Cañada was built in 1733 making it one of the oldest surviving churches in the United States.
There are two side chapels, one in each of the church transepts. The north chapel is dedicated to Nuestra Señora de Carmen (Our Lady of Mount Carmel). The south chapel is dedicated to San Francisco de Asis. It is sometimes called the Chapel of the Penitentes.