Following 80 years of Spanish occupation, Pueblo Indians in northern New Mexico revolted in 1680, driving out the Spaniards for a 12-year period. Spanish refugees, as well as some indigenous New Mexico Puebloans, followed the Rio Grande southeast to the El Paso del Norte area, where they established missions and new settlements.  

On October 13, 1680, the Franciscans founded Mission Santa Maria de Socorro del Sur. The original site is unknown. By 1684, the Socorro residents were using a temporary church at this location. A permanent mission church was constructed here by 1691 and dedicated as Nuestra Senora de la Limpia Concepcion de los Piros de Socorro del Sur, meaning "Our Lady of Immaculate Conception of the Piros of the Socorro of the South."  

The church was adobe construction, with vigas, or wooden beams, supporting the roof. A Piro Indian pueblo stood about 600 feet northeast of the church, and the mission settlement was comprised of Spaniards and Piros, as well as Tano and Jemez Indians. Records indicate the site was used until the 1740s, when flooding destroyed the building. The mission was rebuilt, but after another flood in 1829, the channel of the Rio Grande shifted to the south toward Mexico, and the present Socorro mission was built in the 1840s one half mile northwest of this location.  

Scholars associated with the University of Texas at El Paso conducted archeological investigations in the early 1980s. Discoveries included the remains of church walls, indicating it was built on a cruciform plan, as well as artifacts dating to as early as the 1680s. Today, the early mission site, the oldest known mission site in Texas, is protected as a State Antiquities Landmark.