That alone makes it unusual. What makes it quietly strange is the crypt beneath the chancel, a vaulted chamber whose existence is owed entirely to the slope of the ground, the hillside dropping away sharply enough to permit an entire undercroft beneath the east end of the church. Local tradition held that nuns were buried there, though the crypt is now paved with MacDonnell family graveslabs from 1799, and whatever earlier burials it may have contained are unrecorded. The pointed vault inside still carries impressions of the wicker framework used to support it during construction, a technique known as wicker centring, in which woven branches acted as temporary shuttering for the wet mortar.

The nunnery was founded in the 1180s, probably by Donal Mor O'Brien, and followed the rule of St Augustine. Its earliest reliable documentary appearance is in the Annals of Inishfallen for 1260, which records the death of Slaney, described as O'Bryan's daughter and abbess of Kill Eoin, and praised as chief in devotion, alms-deeds and hospitality of all women in Munster. Slaney is thought to have been the sister of Donchad Cairbreach, king of Thomond, who founded Ennis Friary nearby. The house was dissolved by the Crown in 1584, and thereafter slipped from the documentary record. A satirical poem written in 1617 offers one memorable glimpse of its final years as a functioning community: it describes Lady Honora O'Brien, who had followed the religious life at Killone in her youth but ran off with Sir Roger O'Shaughnessy, had two children with him, and eventually received papal dispensation for their marriage. By the seventeenth century the buildings were already ruinous, and they have remained so since.

The complex is built around a small near-square cloister, with the church along the northern side constructed from coursed limestone. The east range survives best, preserving several small windows including a double ogee-headed light from the fifteenth century, a style in which the top of each opening curves in an S-shape. The east window of the church is a two-light transitional example with a wall-walk running through it, accessible from a doorway in the north wall of the east end. The site is reachable only on foot, approaching through gates roughly one kilometre to the north or south at the edge of the Newhall estate, and a holy well lies around 200 metres to the east of the abbey.