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Geographical explorations and the subsequent intensification of external commerce made many political actors of the sixteenth and seventeenth centuries AD drag in religion and its various institutions as pliable devices for strengthening their claims of monopoly and control over the political and commercial life of the newly discovered regions. In the midst of these developments, the pre-colonial struggles for appropriating surplus from the European possessions in Asia were at times in the form of struggles between different religious institutions and administrative machineries within the same belief system professed by the various European powers. These conflicts often arose when some of the religious institutions, which were devised at different points of time in history to transmit various types of spiritual experiences to the believers, were appropriated by power-mongers for realizing their political and economic agenda. One of the religious institutions that were often utilized for political purposes during the early modern period was the church administrative system of patronage or the Patronato that the Spaniards introduced in America and the Padroado Real that the Portuguese set up in Asia. As per the right of patronage that the Pope conceded in AD 1455, the Portuguese Crown became the sole authority that could send missionaries to the lands controlled by the Lusitanians, which eventually created a certain type of monopoly for them in matters of Christianity in areas under their influence and kept missionaries of other nationalities out of Asian and Brazilian soil. When the religious issues in Asia began to get increasingly embroiled in the politics of the times, thanks to the dominance of Lusitanian interests in the Padroado system, Pope Gregory XV devised the Propaganda Fide in AD 1622 as an alternative church administrative system for Asia, which in fact was meant to provide opportunities basically for non-Portuguese people, both Indians and Europeans, for missionary work in Asia. However, this led to a chain of conflicts between the ecclesiastical administrative institutions of the Padroado Real and those of the Propaganda Fide, in Asia in general and India in particular, where the core issues of contestation began to revolve around matters of politics and the exercise of power. The central purpose of this article is to examine the nuanced nature of the conflicts that arose between the church administrative systems of the Padroado and the Propaganda at different points in time and also to see how the religious conflicts were appropriated and politicized by the various European colonial powers to further their politico-economic agenda in India.