In the overlay of Muslim and Christian geopolitical interest zones in the early modern Philippines, the missionaries of the Society of Jesus got to play a unique role as cultural intermediaries. This article analyzes some outstanding episodes of Jesuit diplomatic activities between the Spanish colonial government and the rulers on the islands of Mindanao and Jolo. In the setting of the Southeast Asian world, Spain found itself in a hostile environment in which the Muslim polities were a permanent factor. Slave raiders from both islands threatened the coastal villages of the Spanish Visayas, while on the other hand, Spanish imperial plans compromised the sovereignty of the sultans. By investigating Jesuit chronicles and additional contemporary sources, this study focuses on the Spanish side of this relation. It will contextualize the role of the Jesuits as ambassadors and, at the same time, as promoters of their own missionary interests. Thereby, it will assess the geostrategic considerations of the Jesuit order and their similarities with and differences from those of the colonial government in Manila. This article argues that in spite of a general overlap of interests, discrepancies existed and increased over the years, eventually effecting the outcome of negotiations.