It held a piscina, the stone basin used by a priest to wash his hands and rinse the sacred vessels during Mass, and although the basin itself has now sunk below ground level, the recess remains: roughly 0.7 metres deep, with a neatly chamfered pointed arch framing the empty space. It is the kind of detail that speaks quietly about liturgical life continuing here long after the wider structure began to fail.

The church at Kilnaglory is a rectangular building, approximately eight metres north to south and eighteen metres east to west, positioned at the centre of the surrounding graveyard. Only portions of the south and east walls survive, along with the east end of the north wall, and even those are fragmentary and ivy-clad. The gaps in the east and south walls mark where windows once sat; part of a window embrasure survives near the east end of the south wall, and a doorway embrasure can still be made out near the west end of the same wall. The surviving features are broadly late medieval in character. The building was in partial repair in 1615, suggesting it was already in a weakened state by then, and was repaired again between 1699 and 1704. By 1745, according to Brunicardi writing in 1913, it had fallen entirely out of use. That arc of decline, from partial repair to abandonment in little over a century, was common enough for rural parish churches in post-Reformation Ireland, where shifting congregations, changing land ownership, and the disruptions of the seventeenth century left many buildings without either congregation or upkeep.