This article examines the series of debates concerning the status of the Roman Catholic Church in the revolutionary Philippines and in doing so demonstrates the contested legacies of the Patronato at the end of Spanish colonial rule. The government of Emilio Aguinaldo in 1898, which in 1899 was inaugurated as a republic, sought to exercise the prerogatives of ecclesiastical patronage as it had been under Spain. By formally regulating and controlling ecclesiastical appointments, the Philippine state addressed the long-standing issue of ecclesiastical secularization (the transfer of parishes from the regular clergy to the secular clergy) that pitted Spanish friars against Filipino diocesan priests, spurring the nationalist movement in the mid-nineteenth century. In effect, the Aguinaldo government assumed the functions of patronage to ensure the fulfillment of nationalist aspirations. Nevertheless, the status of Catholicism in the new nation-state was debated by Filipino laity and clergy even beyond the center of the revolution. Filipino clergy, for their part, almost unanimously rejected government oversight of ecclesiastical affairs despite demanding church-state union and continued government support. Ecclesiastical affairs in this period were in a constant state of flux, negotiation, and dialogue, underscoring the complex and contested legacy of patronage after Spanish rule.