Spain's colonies in the New World were, legally, the personal patrimony of the king, and he held absolute control over all matters in Ecuador. Colonial administration at all levels was carried out in the name of the monarch. The king's chief agency in Madrid was the Council of the Indies, which devoted most of its energies to formulating legislation designed to regulate virtually every aspect of colonial life. The House of Trade, seated in Seville, was placed in charge of governing commerce between Spain and the colonies. In America, the king's major administrative agents were the viceroyalty, the audiencia [court], and the municipal council [cabildo].

Between 1544 and 1563, Ecuador was an integral part of the Viceroyalty of Peru, having no administrative status independent of Lima. It remained a part of the Viceroyalty of Peru until 1720, when it joined the newly created Viceroyalty of Nueva Granada; within the viceroyalty, however, Ecuador was awarded its own audiencia in 1563, allowing it to deal directly with Madrid on certain matters. The Quito Audiencia , which was both a court of justice and an advisory body to the viceroy, consisted of a president and several judges [oidores]. The territory under the jurisdiction of Quito considerably exceeded that of present-day Ecuador, extending southward to the port of Paita in the north of present-day Peru, northward to the port of Buenaventura and the city of Cali in the south of present-day Colombia, and well out into the Amazon River Basin in the east. Quito was also the site of the first [founded in 1547] and most important municipal council within the area comprising modern-day Ecuador. It consisted of several councilmen [regidores] whose extensive responsibilities included the maintenance of public order and the distribution of land in the vicinity of the local community.

The borders of the Audiencia [or kingdom as it was also known] of Quito were poorly defined, and a great deal of its territory remained either unexplored or untamed throughout much of the colonial era. Only in the Sierra, and there only after a series of battles that raged throughout the mid-sixteenth century, was the native population fully subjugated by the Spanish. The jungle lowlands in both the Oriente and the coastal region of Esmeraldas were, in contrast, refuges for an estimated one-quarter of the total native population that remained recalcitrant and unconquered throughout most or all of the sixteenth and seventeenth centuries. Despite Orellana's harrowing journey of discovery, the Oriente remained terra incognita to the Spanish until its settlement by Jesuit missionaries beginning in the mid-seventeenth century, and it continued to be largely inaccessible throughout the remainder of the colonial period.

The coastal lowlands north of Manta were conquered, not by the Spanish, but by blacks from the Guinean coast who, as slaves, were shipwrecked en route from Panama to Peru in 1570. The blacks killed or enslaved the native males and married the females, and within a generation they constituted a population of zambos [mixed black and Indian] that resisted Spanish authority until the end of the century and afterwards managed to retain a great deal of political and cultural independence.

The relative autonomy of this coastal region nearest to Quito enhanced the effect of the Andes in isolating the Ecuadorian Sierra from the rest of the world during most of the nearly three centuries of colonial rule. Behind these barriers a social system was established that was essentially a replica of the Spanish feudal system at the time of the conquest, with the peninsulares [Spanish-born persons residing in the New World] being the ruling, landed elite and the Indians being the subject people who worked the land. Although a few towns, particularly Quito, Riobamba, and Cuenca, grew along with the administrative and Roman Catholic bureaucracies and the local textile industries, colonial Ecuador was essentially a rural society.

The most common form in which the Spanish occupied the land was the encomienda . Settlers were granted land, along with its inhabitants and resources, in return for taking charge of defending the territory, spiritually indoctrinating the native population, and extracting the crown's annual tribute [payable half in gold, half in local products] from the encomienda 's Indian population. By the early seventeenth century, there were some 500 encomiendas in Ecuador. Although many consisted of quite sizable haciendas, they were generally much smaller than the estates commonly found elsewhere in South America. A multitude of reforms and regulations did not prevent the encomienda from becoming a system of virtual slavery of the Indians, estimated at about one-half the total Ecuadorian population, who lived on them. In 1589 the president of the audiencia recognized that many Spaniards were accepting grants only to sell them and undertake urban occupations, and he stopped distributing new lands to Spaniards; however, the institution of the encomienda persisted until nearly the end of the colonial period.

Land that was less desirable was never distributed, but rather was left to traditional Indian communities or simply remained open public land. In the late sixteenth century, the estimated one- quarter of the total native population on such public lands was resettled into Indian towns called reducciones in order to facilitate the collection of the Indians' tribute, their conversion to Christianity, and the exploitation of their labor.

Outside the encomienda,