New geochemical data are presented for the composite units of the Mount Kinabalu granitoid intrusion of Borneo and explore discrimination between crustal- and mantlederivedgranitic magmas. The geochemical data demonstrate that the units making up this composite intrusion became more potassic through time. This was accompanied by an evolution of isotope ratios from a continental-affinity towards a slightly more mantle-affinity (87Sr/86Sri ~0.7078; 143Nd/144Ndi ~0.51245; 206Pb/204Pbi ~18.756 for the oldest unit compared to 87Sr/86Sri ~0.7065, 143Nd/144Ndi ~0.51250 and 206Pb/204Pbi ~18.721 for the younger units). Oxygen isotope ratios (calculated whole-rock δ18O of +6.5–9.3‰) do not show a clear trend with time. The isotopic data indicate that the magma cannot result only from fractional crystallisation of a mantle-derived magma. Alkali metal compositions show that crustal anatexis is also an unsuitable process for genesis of the intrusion. The data indicate that the high-K units were generated byfractional crystallisation of a primary, mafic magma, followed by assimilation of the partially melted sedimentary overburden. We present a new, Equilibrated Major Element – Assimilation with Fractional Crystallisation (EME-AFC) approach for simultaneously modelling the major element, trace element, and radiogenic and oxygen isotope compositions during such magmatic differentiation; addressing the lack of current AFC modelling approaches for felsic, amphibole- or biotite-bearing systems. We propose that Mt Kinabalu was generated through low degree melting ofupwelling fertile metasomatised mantle driven by regional crustal extension in the Late Miocene.