The mission was built as one of the four missions among the Piro Pueblos between 1615 and 1626 through the Camino Real. This mission was partly destroyed after the Pueblo Revolt and only portions of the old church remains, including parts of the adobe walls and beams. Many preservation efforts have been seen in the mission building, being the most extensive during the 1960s. Today it is a living parish that serves a vast community.
Franciscan missionaries established Mission Santa Cruz de San Sabá in 1757 to Christianize the eastern Apache Indians. The site, rediscovered in the fall of 1993 and proved by archeologists in January 1994, is on the San Saba River about three miles east of the present town of Menard and four miles from the ruins of San Luis de las Amarillas Presidio, which was built to protect the mission.
Mission San Juan Capistrano was established in 1731 and underwent several building periods. The complex has the traditional plan of buildings and walls surrounding a central courtyard and includes the ruins of the second and third church, the foundations of some of the residential quarters, a convento (missionary quarters), granary foundation, well, and a residence.
The church is architecturally significant as physical evidence of building practices and techniques used during the Spanish colonial period. It is the least altered of all the Texas mission churches and has the only original dome of those in San Antonio.