After the victorious revolt, Pope installed himself in the Governor's palace adorned with gaudy clothing and a bull's horn on his forehead to symbolize power. He was viewed with suspicion for his flamboyant actions, which did not portray the valued characteristics of pueblo behavior. Pope rode through the streets of Santa Fe in Otermin's carriage and ordered parodies of Spanish feasts and customs. His leadership is still questionable to the people of the pueblos, but in the short period of the absence of Spanish rule, all churches were destroyed along with all vestiges of Christianity, including Christian names and marriages. Wearers of the crucifix were returned to their original state by a cleansing with yucca soap. In Santa Fe, Spanish buildings were replaced by pueblo houses and kivas. Pope ordered all Spanish crops to be burned and plants such as onions, grapes and peppers, fruits, as well as wheat were ripped up; the pueblo diet would be returned to the basic three; squash, corn and beans. Spanish livestock was slaughtered and their horses released into the hands of the Ute and Apache. Yet, in spite of Pope's actions, as well as his alleged connections with spirit world, the forever present drought continued, reducing the new pueblo empire to just a few dozen shriveled towns between Taos and Albuquerque in addition to Acoma, Zuni and, at the furthest point, Hopi.

In 1692 , a bloodless re-conquest was led by Don Diego Jose de Vargas Zapata Lujan Ponce de Leon y Contreras. By then, after only eight years as sovereign, Pope was dead, some think at the hands of his own disgruntled insurrectionists. The new leader of the pueblos, Tupatu, was summoned by de Vargas and together they conferred. Tupatu promised his support in returning the pueblos to Spanish allegiance. Over the next year, with intermittent loving kindness and merciless determination, Vargas systematically recaptured each of the pueblos. Nevertheless, beset with problems of drought and famine, Spanish and Indian alike perished in the desert land. Although Vargas succeeded in reestablishing Spanish rule, Indian labor was no longer exploited as before. Livestock was also reintroduced as was the two wheeled cart, which revolutionized transport. The adoption of the Spanish language organized communication between different language groups, though Native languages were then and are still widely used in t