While English colonies in the Chesapeake grew and prospered with the tobacco trade, the northern outposts of the Spanish empire in New Mexico and Florida stagnated. Only about fifteen hundred Spaniards lived in Florida, and roughly twice as many inhabited New Mexico, yet both colonies required regular deliveries of goods and large subsidies. One royal governor complained that “no [Spaniard] comes … to plow and sow [crops], but only to eat and loaf.”

Instead of attracting settlers and growing crops for export, New Mexico and Florida appealed to Spanish missionaries seeking to convert Indians to Christianity. In both colonies, Indians outnumbered Spaniards ten or twenty to one. Royal officials hoped that the missionaries’ efforts would pacify the Indians and be a relatively cheap way to preserve Spanish footholds in North America. The missionaries baptized thousands of Indians in Spanish North America during the seventeenth century, but they also planted the seeds of Indian uprisings against Spanish rule.

The missionaries followed royal instructions that Indians should be taught “to live in a civilized manner, clothed and wearing shoes … [and] given the use of … bread, linen, horses, cattle, tools, and weapons, and all the rest that Spain has had.” In effect, the missionaries sought to convert the Indians not just into Christians but also into surrogate Spaniards.

The missionaries supervised the building of scores of Catholic churches across Florida and New Mexico. Adopting practices common elsewhere in New Spain, they forced the Indians both to construct these churches and to pay tribute in the form of food, blankets, and other goods. Although the missionaries congratulated themselves on the many Indians they converted, their coercive methods subverted their goals. A missionary reported that an Indian in New Mexico asked him, “If we [missionaries] who are Christians caused so much harm and violence [to Indians], why should they become Christians?”

The Indians retaliated repeatedly against Spanish exploitation, but the Spaniards suppressed the violent uprisings by taking advantage of the disunity among the Indians, much as Cortés did in the conquest of Mexico (see "The Conquest of Mexico" in chapter 2). In 1680, however, the native leader Popé organized the Pueblo Revolt, ordering his followers, as one recounted, to “break up and burn the images of the holy Christ, the Virgin Mary, and the other saints, the crosses, and everything pertaining to Christianity.” During the revolt, Indians desecrated churches, killed two-thirds of the Spanish missionaries, and drove the Spaniards out of New Mexico to present-day El Paso, Texas. The Spaniards managed to return to New Mexico by the end of the seventeenth century, but only by curtailing the missionaries and reducing labor exploitation. Florida Indians never mounted a unified attack on Spanish rule, but they too organized sporadic uprisings and resisted conversion.