The early modern Philippine archipelago is often described as being under the power of a frailocracy with a far-reaching impact. From a microhistorical approach of ecclesiastical contentiousness, I argue that the intermittent clashes between and inside the two pillars of colonial rule—the civil and ecclesiastical powers—belie the church's overarching control over state affairs. The church was not a monolithic unit in the Philippines, but was rather highly fragmented, especially in distant Asian enclaves, and it was not independent, but relied on royal patronage, diplomacy, and transnational networks. Using archival materials, official reports, religious manifestos, and royal appointments and decrees, I focus upon two significant case studies of the two exiled archbishops of Manila, Fray Hernando Guerrero, OSA, and Felipe Pardo, OP, to explore factionalism, negotiation, and microlevel political constellations as a way to approach conflicting church–state relations in seventeenth-century Philippines from a more nuanced perspective.