This chapter explores first the conflictive relationship between Manila’s archbishop and his cathedral chapter, whose members were fiercely opposed to each other in power groups, especially during the interregnum periods, and second, the rebelliousness and disobedience shown by religious orders to their bishops. The need to strengthen the centralized character of the Crown’s authority in the empire’s Asian-Pacific territories via the Church clashed with local particularities that hindered the imposition of the Council of Trent’s principles as well as the establishment of systematic policies of confessionalization from the seat of diocesan power extremity.