The internal structure and emplacement mechanisms of composite plutons are investigated using new field data from the composite Late Miocene granitic intrusion of Mt Kinabalu in northern Borneo. The pluton was emplaced in the upper to middle crust in the Late Miocene at the contact between the ultramafic basement and sedimentary cover rocks. Structural data indicate that emplacement occurred during regional NNW–SSE-oriented extension, challenging tectonic models that involve contemporaneous regional compression. The six major units forming the pluton were accommodated by upward flexure of the cover rocks with most magma pulses emplaced successively beneath their predecessors. However, the irregular 3D internal structure of the pluton also reflects preferential emplacement of successive units along the granite–country rock contact of previous units in preference to the basement–cover rock contact exploited by the initial units. This study highlights the complex emplacement mechanisms and internal structure of composite intrusions and assesses how they differ from models of tabular emplacement.