As a colonial project, the república de indios featured an inherent contradiction between two goals: on one hand, it attempted to transform indigenous peoples into gente de razón (people of reason, a term the Spaniards expediently reserved for themselves), fully conscious of the superiority, value, and potential of Christianity and Spanish habits and mores; on the other, it strove to shield Indians—regarded as minors in legal terms—from the “bad example” given to them by greedy and corrupt Spaniards. This view prevailed in early colonial times; for example, in 1533, the oidor (local Crown representative) Ramírez de Fuenleal rejected a royal proposal for interracial cabildos, on the grounds that Indian officials would be corrupted by participating in them. Some distinguished mendicant priests, such as Vasco de Quiroga in Michoacin and Bartolomé de Las Casas in Vera Paz and Chiapas, attempted to create and maintain isolated, utopian indigenous communities where the Christian faith and a selection of Spanish mores were learned by peaceful and experimental means. By the late colonial period, however, the tide had turned, and Bourbon reformers called for generalized Spanish instruction and acculturation of rural indigenous populations.
A compromise between isolation and acculturation was achieved in the form of a policy of congregaciones (reductions), which began in the 1540s and extended into the early seventeenth century. The congregaciones incorporated Indians living in clustered small settlements into a preexisting or a new settlement with a church building and a resident priest. The resulting demographic center often was promoted to the rank of a cabecera (main township), and an indigenous town council was created. In this manner, the relative segregation of indigenous communities was combined with the social and didactic influence of a select representative—at least in theory—of Spanish morals: the parish priest.
Pueblos de indios in remote areas tended to function as segregated political and territorial units. For example, in remote areas with no resident priests—such as small townships in Yucatán—contacts with the Spanish colonial administration revolved around tribute collection and weekly doctrinal visits by a priest. Occasionally, territorial isolation and minimal numbers of nonindigenous residents afforded some pueblos de indios unusual political and religious autonomy, as in the case of the eight Yaqui townships established and supervised almost exclusively by Jesuits in northwest New Spain. However, major population centers—nominally a part of the república de españoles—attracted substantial numbers of indigenous migrants from neighboring pueblos. These migrants added additional layers to diverse urban communities, already highly stratified in terms of class and status. Therefore, by the mid-seventeenth century many urban centers substantially departed from the idealized repúblicas defined by colonial law. A case in point was the ethnically diverse, expanding category of naborías (semi-indentured servants) composed of Indian migrants to the city of Oaxaca in the seventeenth century.