In a typical claustral layout, the domestic ranges of a monastery cluster to the south of the church, sheltered from the north wind and oriented to catch what light there is. At Innisfallen, the cloister sits to the north of the church, an inversion of the expected order that speaks to the particular pressures and priorities of the community that shaped this place over several centuries.

The oldest visible fabric belongs to a church that may date to the tenth century, its western two-thirds still showing the characteristic antae, projecting continuations of the side walls beyond the gable end, that mark early Irish ecclesiastical building. A lintelled doorway with inclining jambs survives in the west gable, the jambs splaying slightly wider at the base than at the top in a manner typical of early medieval stonework. Built into the splayed interior of one of the east windows is a pillow-stone, a smoothed stone associated with early Christian burial, reused here as ordinary building material and easily missed. Elsewhere in the church, a bullaun stone sits just southeast of the west gable; bullauns are basin-shaped hollows ground into boulders or loose stones, found across Irish ecclesiastical sites and often associated with ritual or medicinal use. A piscina, the small wall-basin used for washing liturgical vessels, survives in the south chancel wall, its eastern stone retaining a damaged roll-moulding that ends in a spiral motif and may originally have come from the chancel arch of the nearby Abbot's Church. The nave and chancel together run to roughly 22 metres in length, and the putlog holes visible in three of the walls suggest a gallery once occupied the western end. The east and north ranges of the cloister survive, the latter possibly the refectory, where a wall recess near a largely destroyed window may represent the base of a mural stair leading to a reader's pulpit, the raised platform from which a monk would read aloud to the community during meals. North of the main ranges, the kitchen building retains a corbelled semicircular oven, partially collapsed, with fire-cracked stones still in place and a quernstone cemented into the structure; a narrow dog-legged flue runs nearby, though it does not connect directly to the oven. A low wall projecting outward from either side of the kitchen's north entrance, which faces the shoreline, may have served as a water-collection enclosure, a practical response to island life that the monks evidently had to plan around as carefully as the liturgy itself.