Both sides in the struggle for Spanish American independence (1808–25) sought the ideological and economic support of the Catholic Church. From the beginning the church hierarchy for the most part supported the royalist cause. Under the patronato real derived from pontifical concessions to the Habsburgs in the sixteenth century, reinforced by Bourbon regalism in the eighteenth century, bishops were appointed by, dependent on and subordinate to the crown. The overwhelming majority were, in any case, peninsulares and identified with the interests of Spain. They also recognized the threat posed by revolution and liberal ideology to the established position of the Church. Bishops whose loyalty to the crown was suspect were either recalled to Spain or effectively deprived of their dioceses, as in the case of Narciso Coll i Prat of Caracas and Jose Perez y Armendariz of Cuzco. Moreover, between the restoration of Ferdinand VII in 1814 and the liberal Revolution in Spain in 1820 the metropolis provided 28 of the 42 American dioceses with new bishops of unquestioned political loyalty. There were, however, a few examples of bishops who clearly sympathized with the patriots – Antonio de San Miguel in Michoacan and Jose de Cuero y Caicedo in Quito – and some opportunists who had no difficulty coming to terms with the victory of the patriots in their region once it was an accomplished fact.

The lower clergy, especially the secular clergy, were predominantly Creole and though divided, like the Creole elite as a whole, more inclined, therefore, to support the cause of Spanish American self-rule and eventually independence.