In the second decade of the 18th century, the Spanish established the Socorro Mission site to provide food and assistance to the early settlers and those traveling the route.

In 1680, the indigenous peoples of northern New Mexico revolted against Spanish rule, causing both the Spanish settlers and the indigenous communities that had allied with them to flee. Some of them arrived at El Paso del Norte, where they founded a new community called Socorro del Sur. There, they used a temporary shelter as a church.

In 1691, the first permanent church was built, dedicated to Nuestra Señora de la Limpia Concepción de los Piros del Socorro del Sur. This church included 17th-century New Spanish architectural styles, with thick adobe walls, cottonwood beams, and corbels.

The abundance of the Rio Grande's waters supported plant and animal life, creating forests, prairies, and wetlands that provided fertile soil for local crops. However, during the wetter years, flooding occurred that destroyed buildings. One of these buildings was the adobe church, which was destroyed by a flood in 1740. It took four years to rebuild, and it served the community of Indian and Spanish residents who settled along the southern banks of the Rio Grande. After the 1829 flood, the communities of Socorro, Ysleta, and San Elizario moved to the northern side of the Rio Grande.

In 1843, the Socorro Mission was rebuilt again, with enormous dimensions and following the architectural traditions of the 17th century, featuring large adobe walls and floors of plaster and clay, emphasizing the roots of the surrounding community. Inside, to the left of the altar, there is a life-sized statue of Saint Michael, donated in October 1845 by the Holguín family.