The mission was founded on February 23, 1720, because Mission San Antonio de Valero had become overcrowded shortly after its founding with refugees from the closed East Texas missions. Father Antonio Margil received permission from the governor of Coahuila and Texas, the Marquis de San Miguel de Aguayo, to build a new mission 5 miles (8 km) south of San Antonio de Valero. Like San Antonio de Valero, Mission San José served the Coahuiltecan Indians. The first buildings, made of brush, straw, and mud, were quickly replaced by large stone structures, including guest rooms, offices, a dining room, and a pantry. A heavy outer wall was built around the main part of the mission, and rooms for 350 Indians were built into the walls.
A new church, which is still standing, was constructed in 1768 from local limestone. The mission lands were given to its Indians in 1794, and mission activities officially ended in 1824. After that, the buildings were home to soldiers, the homeless, and bandits. It was restored in the 1930s and is now part of the San Antonio Missions National Historical Park.
The church facade features from the top: a cross, representing Jesus Christ, St. Joseph (San Jose) holding the infant Jesus, St. Dominic and St. Francis, Our Lady of Guadalupe (the Virgin Mary), and St. Joachim and St. Anne holding the infant Mary.