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The overprinting episodes of porphyry-type and epithermal-type mineralization in the Mankayan District, northern Luzon, Philippines allow an investigation on variation of geochemical signatures with different alteration assemblages. Due to the multiple hydrothermal activities in Mankayan, some older porphyry-type deposits have been overprinted by acid-sulfate alteration that is commonly associated with high-sulfidation epithermal mineralization. In this study, we analyzed metavolcanic basement rocks and dioritic rocks that host porphyry-type mineralization in the Far Southeast deposit, Honeycomb prospect and Christine prospect, which all have near-neutral pH alteration assemblage of illite/muscovite + chlorite ± quartz. We compared their geochemical data with those of the Fatima porphyry deposit, which was overprinted by quartz + alunite ± kaolinite/dickite alteration. Furthermore, we also compared the geochemical data of the metavolcanic and dioritic rocks in the Carmen and Florence prospects hosting quartz-pyrite-gold and enargite veins which overprinted earlier porphyry-type mineralization. N-MORB-normalized multi-element diagrams show that the host rocks preserve negative anomalies of high field strength elements (HFSEs) that are typical of magmas generated in a supra-subduction zone setting. The non-mineralized metavolcanic and dioritic rocks show variable signature of the large ion lithophiles (LILEs), while the altered metavolcanic and dioritic rocks show a more consistent signature. Negative anomaly of Rb is associated with acid-sulfate alteration, while positive anomaly of Rb was observed in the dioritic rocks that have been altered by near-neutral pH fluids. Furthermore, acid-sulfate alteration significantly added LREEs and depleted HREEs compared to the near-neutral pH alteration. Mass changes in altered rocks were determined using the isocon technique. Mass changes are generally more pronounced in the acid-sulfate altered rocks compared to the near-neutral pH altered rocks. The metavolcanic rocks altered to quartz + alunite in Carmen and Florence significantly gained SiO2, Al2O3 and S, and lost Na2O, CaO, MgO and Fe2O3. The dioritic and metavolcanic rocks altered to chlorite + illite in the Far Southeast, Honeycomb, Christine and Fatima porphyry deposits lost SiO2 and Al2O3, while the concentrations of other elements remain relatively unchanged. The pH-dependence of the geochemical behavior of Rb in hydrothermal conditions was utilized to construct new molar element ratios that could differentiate the rocks that underwent K-metasomatism either under near-neutral pH or acidic conditions. The recognition of this behavior could be useful in a routine lithogeochemical analysis that is being used in exploration.