In 1598, Don Juan de Oñate led an expedition up the Rio Grande. He and his settlers stopped at Quarai, near present Mountainair, then continued farther up the river to San Juan Pueblo (north of Española), where he established a colony and mission. Oñate brought ten Franciscan missionaries with him and one of them, Fray Juan Claros, was given charge of the area from Sandia Pueblo south, past Isleta Pueblo.

When Don Pedro de Peralta reached New Mexico in 1609, he initiated missionary work in the Albuquerque area. By that time Spain had realized that mineral wealth was not to be found in the region, but the church saw potential for winning converts and began building new missions.

Fray Estevan de Perea founded a mission church at Sandia Pueblo, and soon after, Fray Juan de Salas founded another mission church at Isleta. In 1634 Fray Alonso de Benavides wrote that the natives were well taught in church doctrine and ways of civilized living. They prayed in their own language, never missed Mass, and counted their sins on knotted strings. The natives also served as teachers and enforced religious discipline. They learned to participate in the Mass and assisted the priests at the altar. The natives were instructed in the sacraments and taught elementary prayers.

They established two smaller institutions, called visitas, at the pueblos of Puaray and Alameda in the area of present-day Albuquerque. They didn’t have resident priests but were served by the padres at Sandia and Alameda

However, the Spaniards expected Pueblo people to abandon their own religious practices. This and other demands led to the Pueblo Revolt of 1680.