The Pan-African Ambalavayal granite intrudes the high-grade metamorphic terrain of northern Kerala, South India and is spatially associated with the Moyar and Calicut lineaments. The pluton was aligned nearly parallel to the northeast–southwest and east–west faults in the basement, consistent with magma ascent along pre-existing deep-crustal lineaments in an extensional tectonic regime. The pluton is characterized by the presence of iron-rich hydrous mafic minerals, primary magnetite, fO2 above the Ni–NiO buffer and high initial emplacement temperatures near 1000 °C. Modal and textural analyses reveal two probable compositional zones within the pluton: outer and inner. Major element variations support this zoning and point to a peralkaline to metaluminous outer zone and a metaluminous to slightly peraluminous inner zone. Both zones exhibit major and trace element characteristics of the A-type granites with the outer zone belonging to the A1 subtype and the inner zone to the A2 subtype of Eby. The trace element trends observed from outer zone to the inner zone suggests that crystal fractionation may have been the dominant process in the generation of high levels of the incompatible elements in the case of inner zone samples. The high initial 87Sr/86Sr ratio (0.7135) and high Y/Nb ratios (Y/Nb > 1.2) are in the range expected for rocks derived from crustal protoliths. A petrogenetic model involving partial melting of a charnockitic, mafic to intermediate lower crust followed by limited fractional crystallization of the magma in a high-level magma chamber is proposed. The enrichment of HFSE and REE (except Eu) in the inner zone is considered the ultimate product of crystal–melt and volatile activity during the final stage of crystallization in a highly silicic (SiO2 > 74 %) magma chamber.