One was tucked into the base of the nave's north wall; the other was reused as a window sill when a round-headed east window was inserted in the late twelfth or early thirteenth century, literally embedding an older form of writing into new construction. By the time a mid-seventeenth-century parish map terrier recorded 'the walls of a decayed Church' at Churchclara, the building had already lived several lives layered on top of one another.

The oldest part of the structure is the chancel, a pre-Romanesque church built in the early medieval period and dedicated to St Colmán Cláraig, who died in 749. Its east gable is constructed in antae, meaning the side walls project slightly beyond the end wall, a characteristic feature of early Irish church architecture. This original church was later absorbed as the chancel of a larger parish building, with a nave added alongside it. The institutional history became more complex in the thirteenth century: in 1230, Peter, Bishop of Ossory, granted half the rectory of Clara to the Canons Regular of St John's Abbey in Kilkenny, and in 1315 Bishop William extended the arrangement by granting them the vicariate of the parish as well. Inside the church, an aumbry, a small recessed wall cupboard used to store liturgical vessels, survives at the east end of the chancel's south wall. Four corbels at the west end of the nave once supported a gallery, though the west gable is now badly cracked and only partly standing.

The graveyard surrounding the ruins holds its own accumulation of objects. Two bullaun stones, boulders with one or more rounded depressions worn or carved into them and associated with early ecclesiastical sites, are present, along with a fragment of a font shaft and a graveslab dated to the thirteenth or fourteenth century. Several nineteenth-century memorials, including headstones and an altar tomb, sit among the collapsed interior masonry. A holy well lies roughly 65 metres to the north-west of the church, completing a cluster of features that, taken together, mark this as a site of continuous religious significance across well over a thousand years.