What emerged was a souterrain, an artificially constructed underground structure typically associated with early Christian-period settlements in Ireland, used for storage, refuge, or both. This particular example turned out to be unusually complex, a two-chambered structure whose layout only became clear once archaeologist J.P. McCarthy investigated it the following year.

McCarthy's investigation revealed two long stone-built chambers set at right angles to each other and connected by a narrow earth-cut creepway, the kind of low, tight passage that forces anyone moving through it to crouch or crawl. Chamber 1 runs roughly northwest to southeast and measures 7.2 metres in length, 1.2 metres wide, and 1.5 metres high. A small earth-cut cell, barely 0.8 metres in each dimension, sits at its southeastern end, reached by a separate creepway; McCarthy considered this compact cell to be the original entrance to the whole system. A second creepway towards the northwestern end leads into Chamber 2, which is slightly larger, reaching a maximum height of 2 metres and running 7.7 metres along a northeast to southwest axis. Its floor slopes downward towards the northeastern end, and its southwestern end is cut from clay rather than built from stone. The overall arrangement suggests careful planning rather than opportunistic digging, with the right-angle junction between the two chambers and the concealed entry point both serving to complicate access for anyone unfamiliar with the interior. The souterrain has since been closed up, leaving the hillside at Kilclogh looking much as it did before that plough changed everything.