New geochemical data are presented for the composite units of the Mount Kinabalu granitoid intrusion of Borneo and explore discrimination between crustal- and mantlederived granitic 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 by fractional 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 of upwelling fertile metasomatised mantle driven by regional crustal extension in the Late Miocene.