Mission San José y San Miguel de Aguayo was founded in 1720 along the San Antonio River within homelands of diverse Indigenous peoples. Franciscan missionaries and Spanish officials intended it to extend colonial settlement, Christianity, and imperial authority in northern New Spain. The first location was later changed, and the mission complex grew into a walled community with a church, living quarters, workshops, fields, and an irrigation system. Its story begins with Native communities that already knew and used this landscape long before the Spanish arrived.

People from different Native groups entered the mission for reasons that included protection, food, and survival amid disease, conflict, and colonial disruption. They supplied much of its labor and knowledge, while the mission imposed new religious practices and social controls. The name Coahuiltecan is often used for peoples in this region, but it groups distinct communities under an outside label. Residents cultivated crops, tended animals, made goods, and maintained family and cultural ties in ways that cannot be reduced to the missionaries' written accounts.

The present stone church is a later building than the mission's founding and was substantially completed in the late eighteenth century. Builders and craftspeople created its ornamented facade, carved stonework, and surrounding structures over years of work. A water-powered gristmill, the acequia system, and fields show how the mission's economy relied on land and water as much as on ceremony. Secularization in the nineteenth century changed the ownership and use of mission property as the Spanish colonial system waned and the region passed through Mexican and then American sovereignty.

Parts of the complex fell into ruin, and twentieth-century preservation and reconstruction reshaped the visitor experience. The mission became part of San Antonio Missions National Historical Park, while the church remained an active Catholic parish. The wider San Antonio mission group was inscribed as a UNESCO World Heritage Site in 2015. Surviving masonry, reconstructed sections, archaeological deposits, and contemporary worship each represent a different chapter; visitors should not treat every wall as untouched eighteenth-century fabric.

Today the National Park Service operates the visitor center and interprets the mission landscape, while parish life continues in the church. Tours and exhibits explain how Indigenous labor and Spanish colonial ambition shaped the complex and how descendant communities remain part of its story. Walking the enclosure, acequia, and mill connects the architecture to food production, coercion, faith, adaptation, and long-term stewardship of this South Texas place.