The western two-thirds of the nave belong to an older structure entirely, one that predates the Augustinian community and quietly contradicts the building around it.

Innisfallen is one of 24 islands scattered across Lough Leane, the largest of the Killarney lakes, and covers roughly 4.8 hectares. The earlier church is identifiable in part by its antae, a feature of early Irish ecclesiastical architecture in which the side walls of a building are extended slightly beyond the end walls, creating shallow projecting flanks. This construction method had largely fallen out of use before the medieval period, which helps place the original structure in an earlier phase of Irish Christianity. The Augustinian house that incorporated and extended these remains brought the site into the broader current of reformed monastic life that spread through Ireland from the twelfth century onward, but the older core survived, absorbed rather than replaced.