San José y San Miguel de Aguayo Mission, one of the five Spanish missions in San Antonio, was founded in the early eighteenth century as a result of a shift of missionary effort from East Texas to South Texas. In 1719 war between France and Spain resulted in the temporary withdrawal of Spanish missionaries from the East Texas missions. Father Antonio Margil de Jesús, president of the Franciscans of the College of Nuestra Señora de Guadalupe de Zacatecas, went to San Antonio, where, on December 26, 1719, he requested that a new mission be founded. The Marqués de San Miguel de Aguayo, governor of Coahuila and Texas, responded by issuing a decree on January 22, 1720, which authorized Capt. Juan Valdez, alcalde at the presidio of San Antonio de Béxar, to select a suitable site for the mission. On February 23 Valdez, assisted by Capt. Lorenzo García, presented a large tract of land on the east bank of the San Antonio River to Margil, downstream from San Antonio de Valero Mission. The land was assigned to about 240 Indians from an area not far south of San Antonio, mainly Pampopa, Pastia, and Sulujam, the first bands to reside at the mission. Margil entrusted their care to fathers Agustín Patrón and Miguel Núñez de Haro. Núñez moved the mission across the river probably before 1730, the year Brig. Gen. Pedro de Rivera y Villalón officially noted that the church and other structures were now on the west bank. After a disastrous epidemic in 1739 reduced the number of Indian inhabitants to forty-nine, the mission was moved to its present location on higher ground, more than one-half mile from the former site. Numerous Indian groups were represented at San José. Because the baptismal, marriage, and burial registers-the most reliable sources of information about the identities of Indian inhabitants-are apparently lost, probably no more than half of the groups represented can be identified. Of the twenty-one groups known to have stayed at San José, many were Coahuiltecan, though other cultural and linguistic groups were also represented. Among the Coahuiltecans were Aguastaya, Aranama, Camama, Cana, Chayopin, Mayapem, Mesquite, Queniacapem, Saulapaguem, Tacame, Tenicapem, and Xuano Indians. The Cujans were a Karankawan group, the Eyeish were Caddoan, and the Lipan Apaches were Athabascan. Also present were Indians called Borrado and Pinto, collective designations that Spaniards gave to groups of diverse origins who originally lived south of the Rio Grande in Nuevo León and Tamaulipas. Displacement, fragmentation, population decline, and Apache hostility often prompted Indians to seek refuge among the Spaniards. The Spanish themselves-notably through such massive colonization efforts as that of José de Escandón-exacerbated the material problems that encouraged the Indians to move to the missions.
The mission was to acquaint the Indians with Christian teaching, European values, and vocational skills and to convert them to useful citizens of the empire. Neophytes learned the basic tenets of Catholicism, arts and crafts, and music and singing. Juan Agustín Morfi wrote in the 1780s, "many play the harp, the violin, and the guitar well, sing well, and dance the same dances as the Spaniards." Colonial art was exemplified by architecture and sculpture, fresco painting, window masonry, woodwork, and metal craftsmanship. Vocational training was basic to the mission economy and to development of essential livestock and agricultural industries. Father Ignacio Antonio Cyprián's 1749 report noted 2,000 cattle and 1,000 sheep on the mission ranch (El Atascoso). Nine years later, Governor Jacinto Barrios y Jáuregui reported that San José owned 1,000 branded cattle and 3,276 sheep. In 1768, 1,500 yokes of oxen were still on the ranch, according to Father Gaspar José Solís's report, as well as many horses and 5,000 sheep and goats. Indian vaqueros, skilled at cutting mounts, cared for the large livestock, while Indian shepherds watched over the mission's small livestock. The Indians learned fundamental agricultural technology, notably systematic cultivation of the soil, selective use of seed, irrigation techniques, the use of hydraulic power in a flour mill, and granary storage methods. Cyprián recorded that 2,400 bushels of corn were harvested on mission farmlands, and Barrios noted an increased harvest of 4,000 bushels in 1758. Solís noted abundant crops of corn, beans, lentils, potatoes, sugar cane, cotton, melons, and fruit. In 1777 Morfi described the farmlands as an area of about a square league watered by an aqueduct system and producing vegetables and fruit, with peaches weighing up to a pound.
Around April 27, 1721, when Aguayo visited San José at its first site, 227 Indians resided in the mission compound. The compound measured about 332 feet on a side and included temporary religious and secular structures. Father Pedro Ramírez de Arellano, given charge of San José in 1759, launched construction on the present church in 1768. According to Morfi, when the church, with its belfry, choir loft, nave, and vaulted roof, was near completion in 1777, San José was "the first mission . . . in point of beauty, plan, and strength." The cupola and façade were heavily ornamented with colorful geometrical designs. The church was richly embellished with carving and statuary. As the center for religious and social development, it was the place for the Mass, an assembly hall, and a building for baptisms, weddings, and funerals. The stone friary, started in the 1740s, was probably constructed as a series of units built eastward from the church wall and, with its gardens, had a circumference of about 416 feet. Other structures included a granary, a carpentry shop, a blacksmith shop with a dwelling for the smith and his family, and a weaving workshop. The mission pueblo was probably an open village through 1758, but a major change occurred by 1768, when, according to Solís, it was converted into an enclosed defensive compound, probably because of Apache hostility. To assure the safety of 350 inhabitants, the mission plaza was encompassed by four stone walls, each having a gateway. From watchtowers all sides and entrances were visible. Indian quarters, constructed from limestone, each consisted of one room and a kitchen and, by 1768, were located mainly along the walls. Father José Pedrajo built a Norse-type flour mill near the north wall. The mill, described in 1794, was powered by hydraulic energy produced by water pressure built in a cistern and channeled to the turbine.
In the summer of 1794 Governor Manuel Muñoz carried out the secularization of San José, a process whereby some of the mission holdings were distributed among proprietors. The new owners consisted of heads of families and unmarried adults among approximately ninety-six mission Indians. The communal life of the Indians declined, even though their spiritual care remained under the Franciscans. After complete secularization on February 29, 1824, San José Church was placed under the care of Father Francisco Maynes, the pastor of San Fernando Church in San Antonio, and the remains of the mission lands and even some secular mission structures were given to civilian settlers. With the departure of the last Franciscan, Father José Antonio Díaz de Léon, in 1824, San José Mission was formally closed after more than a century of service. Beginning about 1813, troops were stationed intermittently at the mission. They caused considerable damage. In 1859 Bishop Jean Marie Odin invited the Benedictines from Latrobe, Pennsylvania, to reopen the mission for services. Father Alto S. Hoermann restored parts of the friary. The church was reopened for the liturgy and remained open until 1868, when the Benedictines were recalled by their archabbot. Following storms, part of the north wall of the church and the dome and the roof collapsed in December 1868. In 1872 the Holy Cross Fathers of Notre Dame began visits to San José and, in spite of the disrepair, faithfully conducted services in the sacristy for nearly fifteen years.
The steps to the bell tower fell in 1903, and the tower itself tumbled down in 1928, although both structures were promptly rebuilt. Bishop John W. Shaw reopened access to the sacristy and approved archeological excavations at San José. In 1932 major restoration was started on the mission structures by the church, the San Antonio Conservation Society, and Bexar County, assisted by the Work Projects Administration and the Civil Works Administration under the supervision of architect Harvey P. Smith. By 1937 the church dome and roof were restored. The Redemptorist Fathers were in charge of the mission from 1922 to 1931. The Franciscans from the Chicago-St. Louis Province were invited to staff the mission parish by Archbishop Arthur J. Drossaerts. In October 1931 the cornerstone of the modern friary near the mission was laid. The Franciscans, after more than a century, had returned to San José. Between 1947 and 1952 Archbishop Robert E. Lucey restored the façade of the church and the ornate sacristy window, known as the Rose Window, which was designed by Pedro Huizar. Although the structural remains of the mission have been altered architecturally throughout their existence, they exemplify colonial architecture in Texas. Archeological research funded by the Texas Historical Commission was conducted in 1968, 1969, and 1970, disclosing remains of Indian quarters on the north end of the quadrangle. By 1973 preservation studies on San José were being conducted by the National Park Service, the Texas Parks and Wildlife Department, and the Texas Historical Commission. The following year archeological studies exposed foundations of colonial walls. The mission grounds were declared a national and state historical site in 1941 and operated by the Texas Parks and Wildlife Department from 1941 to 1983. On November 10, 1978, San José Mission became part of the San Antonio Missions National Historical Park.