The Pueblos had no single leader so Juan de Onate introduced the office of petty governor (gobernadorcillo) and the smaller governmental positions of lieutenant-governor, sheriff (alguacil), irrigation boss (mayordomo) and church warden (fiscal). Each held a one year term of office after they were elected by a vote of the Pueblo people. This municipal government handled minor political and judicial affairs. Later, a council of elders (principales), comprised of of former governors and lieutenant governors, was added to serve as an advisory committee.

Many specific steps were taken by Spain to solidify its control of New Mexico after initial occupation. Each step gave the Pueblo Indians a governmental and religious structure that would coincide with the Spanish government and religious structure.

These republicas, or municipal domains were the only representative government positions available to the citizens where they were allowed by the Spanish government to participate directly in politics. The flaw in the Spanish system was that the holy men of each pueblo selected who was elected to these offices and then ruled through them. Currently all pueblos still have a governor who leads the government of the Pueblos.

The Spanish made strong attempts to influence the outcome of these elections. They knew who they wanted to lead the pueblo governments and did everything in their power to get that man elected. The missionaries did the same thing.

The religious government and the civil government were constantly maneuvering to get officials elected in the republicas. This struggle for control led to the decline in respect by the Pueblos for the religious government and the civil government.