Yes, even with the introduction of epidemic disease indigenous resistance to colonial encroachment persisted for centuries. Technological “superiority” meant nothing when faced with overwhelming numbers, poor terrain, dedicated resistance, absence of food reserves to support a pillaging army, and a lack of logistical support to maintain frontier outposts. Colonists just labeled their unfinished wars of conquest as rebellion, or revolts, and we inherit a myth that colonization was quick, easy, and inevitable. Here I will adapt a previous response to explain how the paper trail of conquest falsely depicts universally successful conquistadors.

As background, during the exploration and conquest of the New World the Spanish crown sold licenses to explore/conquer/rule a specific region. Adelantados bore the cost of mounting the hazardous expeditions into the unknown, and successful invaders would gain from the production of their land. The crown benefited substantially from selling these grants. Instead of devoting prohibitively expensive military resources to control land in the New World, these contracts placed the financial burden for territorial expansion on would-be conquistadores. The crown gained potential income from new lands, and contractually held the ability to regulate extremes of conquistador behavior if they failed to comply with the terms of the contract. Punishments for abuses or failure to act in a timely manner ranged from imprisonment, to substantial fines, or revoking the original license.

Adelantados were therefore placed under extreme pressure to maintain the resources required for a successful entrada, establish a permanent base of operations, find something that made the new colony immediately economically viable to recoup their losses and continue to hold crown support (hence the preoccupation with precious metals), and convince the crown the local population posed no threat to their endeavors. Lobbying between adelantados and the crown often took years. For example, Juan de Oñate originally submitted a license to conquer New Mexico in 1595, petitioned repeatedly to lobby for contractual fulfillment when the license was revoked in 1597, and then engaged in a prolonged legal battle from 1606-1624 for use of excessive force during the entrada.

Presenting their lands both worthy of conquest and easily conquered emerged as common theme for adelantados attempting to validate their position and maintain continued royal support. The formulaic writing style stressed not only a completely conquered native population, but one willing to submit both to Spanish rule and the Catholic faith, regardless of the actual facts on the ground. Hedged in religious terminology, and with papal support that acted as a divine grant of land for Castile and Portugal, “claims of possession became synonymous with possession itself” (Restall, p.68).

Since conquistadores were fighting rebels against the crown and the Catholic faith, military campaigns were undertaken for pacification (not conquest). Since resistance leaders were rebels they could be tried and executed for treason, their followers legally enslaved for rebellion (despite the official ban on native slavery within the empire). I’ll quote Restall here because I can’t put it better…

This pattern can be seen in the Yucatan as well as in virtually every region of Spanish America. Having founded a new colonial capital in 1542, named Mérida, the Spaniards in Yucatan declared the Conquest achieved and set about “pacifying” the peninsula. But as they controlled only a small corner of it, they were obliged to engage in major military hostilities with one Maya group after another, encountering particularly strong resistance in the northeast in the late 1540s. This was clearly an episode in a conquest war now in its third decade, but just as the Spaniards had already declared the Conquest complete so did they now classify this resistance as a rebellion… This was used to justify the execution of captives, the use of display violence (notably the hanging of women), and the enslaving of 2,000 Mayas of the region. Four centuries later, historians were still calling this “The Great Maya Revolt.” (p. 69)

The myth of a completed conquest protected adelantados from a revoked license, while simultaneously allowing them the legal use of increased force to subdue rebellion. Little wonder conquest narratives adopt an air of inevitability to the process of conquest. Adelantados, local officials, and the greater empire hoped and prayed their military endeavors would succeed. Until they established complete control over lands granted to them by the crown, the rules of the empire rewarded those who maintained the fiction of an uncomplicated, completed conquest. If we inherit an inevitable narrative of conquest it is only because, in hindsight, we read the hopes of adelantados as truth.

Here are a few examples...

• The popular narrative states the Inca Empire fell in 1532 with Atahuallpa’s capture and execution. Some may argue a later completion date when troops loyal to the Inca lifted the siege of Cuzco in 1536. After these setbacks, the Inca established an independent state until the final Inca, Túpac Amaru, was executed in 1572. Instead of rapid conquest won by the great conquistador Pizarro, that is nearly four decades of fighting. Even after Túpac Amaru’s death, large portions of Tawantinsusyu remained well outside Spanish control and continued to violently oppose Spanish encroachment.

• As previously mentioned, the capital of Mérida was established in the Yucatan in 1542, and officially the conquest of the Maya claimed. However, independent polities abounded on the peninsula. Both military conquest, and peaceful Franciscan attempts to incorporate the independent kingdoms, failed. Petén remained independent, and accepted refugees fleeing from Spanish controlled areas. The last independent kingdom, Itza, finally fell in 1697, a century and a half after Spaniards raised the “Mission Accomplished” banner in Mérida. Resistance continued. In 1847 the Yucatan Maya pushed the colonial frontier back to the sixteenth-century limits, and some regions maintained independence into the early twentieth century.

• The Chichimeca War pitted Spanish expansion against the Chichimeca confederacy only eight years after Spain failed to completely extinguish the Mixtón Rebellion. For four decades the Chichimeca attacked neighboring Native Americans allied to the Spanish, as well as caravans in and out of the vitally important mining towns of Zacatecas. Between 1550 and 1600 the conflict cost more Spanish lives than any previous military conflict in Mexico. The futility of military maneuvers against the guerilla tactics used by the Chichimeca required a shift in Spanish methods of conquest. New policies emphasized both the use of missions to establish peaceful trade, as well as the relocation of staunchly loyal Native American allies to both act as buffers to the violence and lead the Chichimeca to docility by example.

• After ninety years of near-constant tension since Oñate’s entrada, the Spanish frontier in New Mexico collapsed in 1680. The Pueblo Revolt ousted the Spanish from New Mexico for twelve years, and jeopardized the entire northern frontier of the empire during a time when the Spanish feared growing French and English encroachment. Diego de Vargas led a “bloodless” reconquest in 1692, but the nature of subsequent Native American-Spanish relationships in New Mexico changed to reflect the constant negotiation and re-negotiation required to maintain an isolated frontier on the edge of a vast empire.

• The Yaqui Wars, started by Spain, and inherited by Mexico, were a source of constant conflict from the late 1600s until 1929. Along with the end of the Caste War against the Maya, the termination of the Yaqui Wars marked the last of centuries of conflict that ranged from the Sonoran desert to the highlands bordering Guatemala, commonly wrapped together under the inclusive title of “Mexican Indian Wars”. The United States likewise inherited a war of incomplete conquest with the acquisition of Spanish Florida. As Seminole history reminds us, some nations never surrendered despite repeated claims of completion.

In North America, a century after initial contact, more than two million people lived east of the Mississippi River. Less than five hundred were European. After more than three hundred years of war, epidemics, displacement, and maneuverings the descendants European colonists finally gained hegemony east of the Mississippi by 1820. Conquest was not inevitable, or easy, or rapid, but rather unfolded over the course of centuries.

For more information check out Seven Myths of the Spanish Conquest for a great introduction.