The Philippine Mobile Belt is a complex plate boundary with multiple terranes in Southeast Asia, yet its early tectonic evolution is still not fully understood due to a scarcity of solid evidence. Here we report new whole rock geochemical, Sr-Nd isotopic, and zircon U-Pb-Hf isotopic data for Cretaceous-Miocene arc magmatic rocks from the Cebu and Bohol Islands, Philippine Mobile Belt. Bulk geochemical data display arc affinities with enriched large ion lithophile elements (e.g., Sr and Ba) and depleted high field strength elements (e.g., Nb, Ta, and Ti). The high positive εNd(t) (+4.6 to +9.1) values and low initial 87Sr/86Sr ratios (0.7032–0.7048) suggest that these igneous rocks were generated by partial melting of mantle wedge in an arc setting. U-Pb dating of zircons revealed Cretaceous (ca. 120–90 Ma), middle Eocene to early Oligocene (ca. 43–30 Ma), and middle Miocene (ca. 14 Ma) crystallization ages for the arc magmatism with abundant Permian-Triassic zircon xenocrysts clustering at ca. 250 Ma. The Permian-Triassic grains show dominantly negative εHf(t) values ranging from −16.2 to −6.6, which are similar to those of coeval rocks in Eastern Indochina. Combined with previous paleomagnetic studies, we propose that an Eastern Indochina-derived continental fragment was involved during the formation of arcs in the Cebu and Bohol Islands, which highlights the potential contribution of ancient continental materials in the formation of intra-oceanic arcs. This scenario does not support the previously proposed model that the Cretaceous arc in the Philippine Mobile Belt formed in the northern margin of the proto-Philippine Sea Plate and Australian margin.