Después del restablecimiento de las misiones en la región, los Zunis se unieron a las luchas armadas del pueblo en 1680 destruyendo a la Misión de la Purísima Concepción, Tanto los Zunis como los españoles abandonaron Hawikuh por completo, sin regresar nunca más. 

The mission was built as one of the four missions among the Piro Pueblos between 1615 and 1626 through the Camino Real. This mission was partly destroyed after the Pueblo Revolt and only portions of the old church remains, including parts of the adobe walls and beams. Many preservation efforts have been seen in the mission building, being the most extensive during the 1960s. Today it is a living parish that serves a vast community.

San Juan Pueblo is known as the first Spanish settlement in the Southwest. After the recolonization of New Mexico by the Spanish in 1692, a mission complex was built to serve the Ohkay Owingeh Pueblo. It consists of parallel blocks of one and two-story adobe houses, rectangular ceremonial kivas, a stone chapel and a 1912 stone church with Gothic Revival elements built on the site of the earlier mission church. San Juan is a living church.