The Boyongan and Bayugo porphyry copper-gold deposits are part of a belt of gold-rich copper deposits in the Surigao district of northeast Mindanao, Philippines. The detailed age relationships described in this study provide insight into the geologically short life cycles that characterize porphyry formation in dynamic arc environments. Since their late Pliocene emplacement (2.3–2.1 Ma; SHRIMP [sensitive high-resolution ion microprobe] U-Pb zircon dating) at depths of 1.2–2.0 km, these deposits were exhumed, deeply weathered, and buried. Weathering of these deposits led to the development of the world's deepest known porphyry oxidation profile (600 m thick) at Boyongan, and a modest (30–70 m) oxidation profile at adjacent Bayugo. This early-middle Pleistocene supergene event followed a period of rapid uplift and exhumation in northeast Mindanao (2.5 km/Ma; [U-Th]/He apatite age-elevation spectrum). Subsequent rapid subsidence (≥0.34 km/Ma; radiocarbon age-elevation spectrum) and burial of these deposits are attributed to a mid-Pleistocene shift from transpressional tectonics to the present-day transtensional setting in northeast Mindanao. During this period, debris flows, volcanic material, and fluviolacustrine sediments accumulating in the actively extending Mainit graben covered the weathered deposits, preserving the supergene profiles beneath 50–500 m of cover. This detailed geochronological study documents the geologically short (<2.3 Ma) time scales over which these major intrusion-centered mineral deposits evolved from emplacement, exhumation, deep oxidation, and burial, highlighting the dynamism of tectonic processes in environments such as the Philippine Mobile Belt.