During excavation within the chapel, archaeologists uncovered a row of four postholes, the soil-filled voids left where upright timber posts once stood, arranged in a line that sits slightly askew to the chapel walls above them. That misalignment is telling: when the famous Romanesque chapel was built in the twelfth century, it was not built in perfect alignment with whatever structure had occupied the ground before it.

The postholes are interpreted as the remains of an early church, a modest timber construction of a kind common in early medieval Ireland before stone became the standard building material. What makes the identification compelling is the behaviour of the dead. Burials belonging to what excavators identified as Phase 2 of the graveyard were found to be oriented in line with this earlier structure rather than with Cormac's Chapel, suggesting that the community burying their dead there was still organising itself around the older building. The phasing was documented by Hodkinson in 1994. No physical trace of the early church survives at ground level today; its existence is known entirely from those four holes in the earth and from the way the graves were laid out around it.