Founded in 1720, this mission was named for Saint Joseph and the Marqués de San Miguel de Aguayo, the governor of the Province of Coahuila and Texas at the time. It was built on the banks of the San Antonio River and founded by Father Antonio Margil de Jesús.
During much of the Spanish colonial period, Santo Domingo was an important Franciscan mission center and the ecclesiastical capital of New Mexico. A mission church erected here before 1607 by Fray Juan de Escalona, was considered one of the largest and finest in New Mexico.
Santa Clara Pueblo was first visited in 1541 by part of Francisco Vásquez de Coronado's expeditionary force. A mission was established in 1628 as a visita for San Juan Pueblo. In 1680 the inhabitants of Santa Clara took an active part in the Great Pueblo Revolt against the Spanish.
Built on a rocky hill for Keresan'speaking people from Acoma, Santo Domingo, and Cohití, this church was constructed with stone and adobe in 1701, following the social upheavals caused by the 1680 Pueblo Revolt.