Secular clergy and missionary religious, each operating under their own organizations, shared responsibility with the Holy Office of the Inquisition for maintaining the faith in Spanish America. While the missionaries aimed at the conversion of pagan Indians and the seculars ministered to the faithful, the inquisitors dealt with religious deviation. Philip II had transferred the Inquisition to the New World in the sixteenth century for this specific purpose. In an empire where religion was an aspect of citizenship at least as important as birth, this responsibility of the Holy Office was indeed a grave one. Non-believers might undermine the faith of Indians and other ‘ignorant persons’ and thus dilute the purity of America. The Laws of the Indies, accordingly, charged the governmental authorities and bishops to rid the Indies of foreigners and other persons ‘suspicious in matters of the faith’. The Inquisition stood as the first line of defense.

Regarding religious conformity, all persons in New Spain were subject to the jurisdiction of the Holy Office. The only exceptions were the Indians, and they came under the less formal and reportedly more lenient episcopal inquisition in the hands of the bishops and the secular clergy. Religious, chiefly Dominicans well schooled in canon law, made up the core of the Holy Office itself. Laymen and churchmen alike aided the inquisitors, and the whole functioned much like any other government agency. The main exception was that Inquisition records and proceedings were closed to inspection by viceregal authorities.