Its walls still stand to their full height, smothered in ivy, and yet beneath the floor lie vaulted crypts inserted by successive generations of one family who effectively took over the building for their own dead. A large stone capstone from one of those crypts sits just inside the doorway, the first thing a visitor would step around on entering.

The structure is likely a medieval chapel of ease or manorial church, a small place of worship built to serve a local lord's household rather than a full parish, associated with the Nugent family who held lands at Clonlost. No church appears at this spot on the 1657 Down Survey map of Rathconnell Parish, which recorded Thomas Nugent as a Protestant landowner on these lands in 1641, so the building may already have been in decline or altered beyond recognition by then. From the 17th century onwards, whatever liturgical function the church had retained was gradually supplanted by its role as a Nugent mausoleum. A chest tomb dated 1672 survives in the south-east corner. In 1710, Thomas Nugent of Cushenstown directed in his will that he be buried 'with his ancestors in the church of Clonlost, where some of his children are buried', and in 1727 Walter Nugent of Carpenterstown made a similar request, asking to be laid in 'his ancestors' burying place at Clonlost'. The building itself is a patchwork of periods. The pointed doorway in the south wall has been reset into an earlier opening, and above the cut-stone arch the rear-arches of the original embrasure are still visible. A trefoil-headed window at the east end of the south wall, likely 14th or 15th century, retains its glazing groove and iron bar socket. Below it sits a small L-shaped aumbry, a niche in the wall once used to store liturgical vessels. A cusped ogee-headed window in the east wall, set into a wide embrasure with sandstone corners, may be even earlier, with a possible 13th-century date suggested by the stonework. The west wall, unlike the north and south walls, is not bonded into them, and is likely a later rebuild, perhaps post-1700, which would also account for the round-headed window set high in that wall and the traces of plaster still visible on its interior face.

The graveyard is set in woodland and was shown on the 1837 Ordnance Survey six-inch map as a pentagonal enclosure, an unusual shape that hints at earlier boundaries predating the surveyor's visit. St Columbkille's Well lies about 110 metres to the south-east, suggesting a cluster of early Christian associations in this part of the parish that the later Nugent presence has rather overshadowed.