San Elizario Chapel, as known as La Capilla de San Elcear, was never a mission, but it functioned as a presidio chapel. It provided the religious needs of a presidio or an outpost of military personnel. The presidio was moved to the present site in 1789, to protect travelers and settlers along the Camino Real (Royal Highway) which ran from Mexico City through Juarez City, Mexico then called Paso del Norte to Santa Fe, NM. Its close proximity to the Ysleta and Socorro missions also provided protection for them.
When Mexico became independent from Spain in 1821, the military presence at the presidio decreased. By 1848, the presidio had fallen into ruins. Rebuilding efforts began in 1853, with a small church. This proved inadequate and the present structure was completed in 1882. The exterior appearance has ever since changed very little.