The church occupies the nave of the former cathedral, a medieval structure that was left partially ruinous and then repurposed in the early nineteenth century. The effect is quietly disorienting: an active parish church fitted into the skeleton of a building that once served a diocese, with centuries of architectural and devotional history layered into its walls and floor.

The cathedral at Kilfenora, dedicated to St Fachtna, was the seat of one of Ireland's smallest dioceses, and its history reaches back into the early medieval period. What the present church inherited when it moved into the nave was not a blank space. Three effigial tombstones, stone slabs carved with the recumbent figures of the deceased, lie in the church's porch. Effigial monuments of this kind were a prestige form of commemoration in medieval Ireland, and finding three of them in a porch rather than formally displayed is itself a reminder of how much was displaced during centuries of change. Inside the nave, a thirteenth-century font survives, a stone basin used for baptism, which predates the present building arrangement by some six hundred years. On the north wall there is a seventeenth-century wall monument associated with the MacDonagh family. Perhaps the most ambiguous survival is a carved head in the south-east corner of the building, which may be a remnant of the former chancel arch, that is, the decorative arch that once divided the nave from the chancel in the original cathedral. If so, it is a fragment of a spatial boundary that no longer exists, preserved almost accidentally in the corner of its successor building.