The Capilla de San Elcear was never a mission, rather it was a presidio chapel, providing for the religious needs of a presidio, or outpost of military personnel. The presidio was moved to the present site in 1789, to protect travelers and settlers along the Camino Real, (King's HIghway) which ran through El Paso to Santa Fe. It is close to the Ysleta and Socorro missions so it provided protection for them as well.
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 is little changed from that time.