This chapter deals with the difficult years of Father Miguel García Serrano’s government at the head of the Archbishopric of Manila (1620–29). He had to face internal challenges, such as the promotion of prebendaries and the succession in vacant sees, and external ones, mainly the visitations of the doctrinas or parishes, the question of the “alternative system”, and the jurisdictional conflicts with the Royal Audiencia. Through political and ecclesiastical microhistory, I show the complex nature of church-state relations and the jurisdictional conflicts between colonial institutions in the cosmopolitan city of Manila.