Many of the early explorations and expeditions into New Mexico passed through the site of what is now Socorro, beginning in 1581. They succeeded in putting the area on the Camino Real from Mexico City to Santa Fe. The town, however, owes its establishment to the 1680 Pueblo Revolt in New Mexico. Spanish and Piro refugees from Socorro, New Mexico, gave the mission and town their name. The mission has had several designations: San Pedro de Alcantará, La Limpia Concepción, La Purísima Concepción, San Miguel, and La Purísima. Governor Antonio de Otermín and Father Francisco de Ayeta, superior of the Franciscans in New Mexico, after leaving some of the refugees at El Paso del Norte (present Ciudad Juárez, Chihuahua), continued several miles southeastward down the Rio Grande to deposit another contingent at Senecú. Spaniards and Tiguas from Isleta, New Mexico, were also asked to remain at Ysleta del Sur, the third stop. The fourth stop was at the site of Socorro, fifteen miles from El Paso del Norte, probably on October 13, 1680. The Franciscan pastor who accompanied the expedition, Antonio Guerra, marked the founding of the town with a Mass that day.
In 1692 Fray Joaquín de Hinojosa, pastor of Socorro, received the royal titles to the first permanent mission and its lands. That year and the next, many Spaniards and a few Piros left to reconquer and settle in New Mexico. In 1693 only fifteen Spanish and sixty Piro families were recorded at Socorro. From 1725 to 1744 a second permanent church was built, dedicated to La Limpia Concepción (the Immaculate Conception). In 1727 the royal visitor general, Pedro de Rivera y Villalón sent a glowing report on the fertility of the region. Four years later Bishop Benito Crespo of Durango administered confirmation there. The statistics for 1734 recorded fifty Piro families; nothing is said about the Spaniards.
In 1744 Fray Juan Miguel Menchero sent a detailed map, a report, and a good sketch of the church. He showed sixty Piros and six Spanish families. In 1750 the official Franciscan visitor recorded forty-three Piro families, who now understood Spanish. In 1754 the Franciscan visitor general, Manuel San Juan Nepomuceno y Trigo, had high praise for the firm faith of the natives, who now amounted to "a few over fifty families." In the ensuing decades the number of Spaniards rose dramatically. In 1760 Pedro de Tamarón y Romeral, bishop of Durango, visited Socorro to administer confirmation. He furnished population statistics and measurements of the church building. He recorded forty-six Indian families for a total of 182 individuals. Including several residents of Tiburcio (present San Elizario), Socorro had eighty-two Spanish families, for a total of 424 persons.
In 1814, by which time soldiers had been withdrawn to fight in the Mexican War of Independence, Socorro comprised sixty-eight Indians and 632 Spaniards. The Rio Grande valley towns became a part of Mexico in 1821. The Constitution of 1824 transferred the El Paso valley from the New Mexican to Chihuahuan jurisdiction. In the spring of 1829 the rampaging Rio Grande swept away the church and homes in Socorro. Henceforth, Ysleta, Socorro, and San Elizario were on the opposite bank of the river, in Texas.
By 1840 the third permanent church was far enough along in construction to be used for services, although it was not completed and dedicated until August 1, 1843. The Texas Revolution of 1836 did not affect the El Paso valley, a part of Chihuahua. The Treaty of Guadalupe Hidalgo (1848) gave the El Paso valley to the United States, but ecclesiastically it continued to be governed from Durango until 1872.
The Jesuits came to Socorro in 1881 and completely reorganized and modernized the associations of men, women, and children. Shortly later Adolph F. Bandelier visited Socorro and reported that all Indians had been completely Mexicanized. The New Mexican Jesuit Juan Córdova was in charge of the mission from 1896 to 1915, and the French Jesuit León Dupont, from 1915 to 1925. Another Frenchman, Gerard Decormé, S.J., made many material improvements during his twenty-one years (1925–46) and wrote several volumes of Mexican and local history. The pastor who was longest in charge (from 1946 to 1978), the Mexican Jesuit Abdón Zúñiga, made many important improvements. The next year Archbishop Patrick Flores transferred the mission from the Jesuits to diocesan priests.
The Mission Heritage Association, 1980–85, with a $50,000 gift from the Texas Historical Commission, was able to save the edifice from collapse. The work was done under the direction of Patrick Rand. An excavation site a mile northwest of the present mission shows findings of an earlier chapel and a small monastery. The date and circumstances of its building and destruction have not yet been determined.