During excavations carried out in 1995, archaeologists uncovered traces of foundation remains belonging to an older structure, one that may itself have been a church, buried beneath what is already an ancient site.

The discovery points to a pattern that recurs across early Christian and medieval Ireland, where sacred sites were rebuilt, enlarged, or repositioned over centuries, each new structure sometimes overlapping or consuming the one before it. At Ballynoe, the foundations came to light beneath the east wall of the nave, the main body of the church, a location that suggests the earlier building occupied broadly the same ground but was aligned or dimensioned differently. Whether the earlier structure predates the standing church by decades or centuries, and what form it took, remains uncertain given the fragmentary nature of what survived. The excavation was documented by Cotter, whose reports from 1996 and 2002 record the find, though the evidence is described as traces rather than anything more complete.