The walls of the nave at Kilquane still stand to over three metres in places, built from large, roughly coursed blocks on a projecting foundation plinth, and the tooling on a single surviving jamb stone at the west doorway points to thirteenth-century construction techniques. The chancel, added later, has its own peculiarity: a base batter, the sloped thickening at the foot of a wall used to increase stability and deflect water, was added to three of its walls at some point, while the south wall appears to have been substantially rebuilt at the same time. A local tradition recorded in the Ordnance Survey Field Book of 1840 described the building as a friary founded by a saint called Cohen or Quain, a detail that has embedded itself in the placename. Scholars have found no corroborating evidence for any such foundation, and the more probable explanation is that this was a straightforward parish church, one absorbed into the orbit of Mourne Abbey sometime in the sixteenth or seventeenth century.

The site sat heavily overgrown until 1993, when members of the local community undertook a clearance and stabilisation effort. Archaeological supervision accompanied the work, and a two-metre trench cut across the chancel revealed an irregular flat-stone floor surface beneath the accumulated rubble. At the north end of the trench, a jamb stone from a window surround came to light, its style consistent with fifteenth-century work, which suggests the chancel was added roughly two centuries after the nave was first built. Only one jamb stone of the door connecting nave to chancel survives; the east gable of the nave is reduced to its lowest courses. The site sits in the northern half of a graveyard, with a holed stone lying about thirty metres to the north-west and a tumulus in a field roughly forty-five metres to the west-south-west, placing the church within a wider, older landscape that the building itself, for all its ruined state, belongs to rather than dominates.