Three missions along the San Gabriel (known at the time as the San Xavier) River, near the site of present-day Rockdale, Milam County, served the Indians of Central Texas from approximately 1746 to 1755. The missions, which included San Francisco Xavier de Horcasitas, San Ildefonso, and Nuestra Señora de la Candelaria, were founded under the sponsorship of the College of Santa Cruz de Querétaro, a Franciscan college in Mexico. The project began in 1745 when a group of Indians visited Mariano Francisco de los Dolores y Viana of the San Antonio missions and asked him to establish a mission for them in their own territory. Indians from the Yojuane, Deadose, Mayeye, and Ervipiame groups agreed to wait for Father Dolores at a site they had chosen for the mission. In the fall, Dolores and the commissary visitor from Querétaro, Father Francisco Xavier Ortiz, met the Indians near the San Gabriel River. Ortiz took the mission proposal to the college while Dolores began converting and teaching the Indians. The college approved the project because the Indians had already congregated, and a new mission would replace the recently secularized Mission Santa María de los Dolores de la Punta at Lampazos, Nuevo León. The college kept Father Dolores's temporary mission, known as Nuestra Señora de los Dolores del Río de San Xavier, supplied while Father Francisco traveled to Mexico City to secure viceregal approval and financial support for the missions. It took several years for the college to get royal sanction for the San Xavier missions. Advocates of the project in Mexico City argued that the missions would form a barrier between hostile Lipan Apaches and the coast, and would discourage trade between the Indians and the French. Opponents claimed that the location was unsuitable for irrigation and difficult to defend against Apache attacks. Moreover, José de Escandón's expedition to the Gulf Coast had already strained Texas defenses. Finding soldiers to protect new settlements would be problematic. Despite such arguments, the college persisted in pressing for approval. Viceroy Francisco de Güemes y Horcasitas, Conde de Revilla Gigedo, finally authorized the college to assign six missionaries to three new missions along the San Gabriel River in December 1747.
Arranging for adequate protection of the San Xavier missions provided the college with a new challenge. The viceroy had approved the transfer of thirty soldiers from the presidios at Los Adaes, San Antonio, and La Bahía in 1748, but local officials in Texas refused to comply with his instructions. Such problems convinced college authorities to recommend establishment of a regular presidio to protect the missions and assist the missionaries in their work. In 1749, Viceroy Revilla Gigedo ordered the governor of Texas, Pedro de Barrio Junco y Espriella, to visit the missions and investigate the need for a presidio. The governor found San Francisco Xavier de Horcasitas and San Ildefonso teaching more than 200 neophytes each. Despite the apparent success of the missions, he disapproved of the need for a presidio and recommended that the missions be moved to a site on the San Marcos River. Before the governor's report reached Mexico City, viceregal officials sanctioned establishment of a regular presidio and sent Capt. José Joaquín de Ecay Múzquiz to locate a site near the missions in early 1750. In his report, the captain described the missions' condition as satisfactory despite inadequate funding and uncooperative troops, who mistreated the Indians and encouraged them to flee. Ecay Múzquiz recorded 153 Indians at San Francisco Xavier, 165 at San Ildefonso, and 90 at Candelaria. He began construction of an irrigation canal for the three missions in October 1750, but it was never finished. The establishment of a formal presidio precipitated the rapid decline of the San Xavier missions. The new commander, Capt. Felipe de Rábago y Terán arrived with fifty new troops in December 1751 to build the presidio, San Francisco Xavier de Gigedo. Unfortunately, the captain took an instant dislike to both the location and the missionaries. The captain's lascivious conduct and his violation of Mission Candelaria's sanctuary led the missionary chaplain to excommunicate the entire garrison. This crisis was resolved, but continuing disagreements between the missionaries and Rábago y Terán led Indian neophytes to desert Candelaria. Shortly thereafter, the mission was attacked by unknown assailants, and Father Juan José de Ganzabal and Juan José Ceballos, a soldier seeking refuge in the mission, were killed. Rábago, implicated in the murders, was replaced by Miguel de la Garza Falcón, who found only Mission San Francisco Xavier still occupied. As a result of the Candelaria attack, the College of Querétaro recommended that the viceroy replace the garrison with a civilian settlement.
No action was taken on San Xavier, but a new mission project to serve the Apaches was being considered. The San Xavier missions struggled on despite a prolonged drought and epidemic. Finally, Father Dolores y Viana proposed in 1753 that the missions be moved; the new presidio commander, Pedro de Rábago y Terán, recommended removal of the missions to San Antonio or San Sabá in 1754. Without waiting for official approval, Rábago y Terán moved the missions and the presidio to the San Marcos River in August 1755. An Apache truce had eliminated the need for a presidio at San Xavier. While the missionaries were at San Marcos, 1,000 Apaches joined the missions. The friars wanted Capt. Rábago y Terán to permit them to move to Apache territory, but he insisted on waiting for royal approval. The following year, the viceroy approved the San Sabá mission project to establish a presidio and missions in Apache territory. San Xavier neophytes were transferred to San Antonio missions, and mission property and the presidio were reassigned to Santa Cruz de San Sabá Mission. A small group of San Xavier Indians, the Mayeyes, did persuade the missionaries to set up a new mission for them on the Guadalupe (see SAN FRANCISCO XAVIER MISSION ON THE GUADALUPE RIVER), but it lasted only until 1758.