The geology of Mynydd Mallaen is complex, comprising mudstones of the Claerwen Group together with sandstones of the Doethie and Glanyrafon Formations and the Caerau Mudstones Formation. Each of these Silurian rock formations is folded and faulted. Indeed it is an outcrop of conglomerate turbidite rock on the western limb of the Cothi Anticline which forms the summit of the hill.