Its formal Latin dedication, Kyrieleyson, is taken directly from the Greek phrase meaning "Lord have mercy," a liturgical cry embedded so thoroughly into the place's identity that for centuries documents referred to it simply by that name rather than by any saint or founder. Half a mile north-east of Abbeydorney village, the remains stand in the townland of Knockaunmore, a quiet corner of the barony of Clanmaurice, and the name of the surrounding deanery, Othorna and Offlanan, itself preserves the memory of two local septs, the Uí Thorna and the Uí Fhlannáin, whose territory this once was.

The monastery was founded in 1154, a daughter house of Monasteranenagh in County Limerick, possibly under the patronage of King Turlough O'Brien of Thomond, and it was affiliated as a sister house to Mellifont in County Louth, the founding house of the Cistercian order in Ireland. Its early history drew in figures of considerable standing: Christian O'Conairce, the first abbot of Mellifont and later bishop of Lismore, resigned his see and retired to O'Dorney around 1179, dying there in 1186. The monastery was drawn into wider controversy in 1227 when its abbot was deposed for involvement in the so-called conspiracy of Mellifont, a period of serious internal disorder within the Irish Cistercian network. By the early fourteenth century the house was wealthy enough that its abbot could serve as a lord in parliament, and in 1307 the abbot was personally dispatched to the deathbed of Maurice of Molahiffe, second baron of Kerry, to carry the dying man's wishes to his son and heir, a role that placed the monastery at the centre of one of Kerry's most powerful feudal families. The abbey was not without its difficulties in the fifteenth century; between roughly 1458 and 1472, Edmund Fitzmaurice held the abbey without any legal title before Philip Stack, archdeacon of Ardfert, was appointed to restore order. After the dissolution of the monasteries, Edmund Lord Kerry was created Baron of Odorney and Viscount Kilmaule in 1537 and granted the abbey's estates. The site then passed through a succession of Crown leases, to Gerald earl of Desmond in 1579, to John Zouche in 1581, to John Champen in 1589, and eventually into the hands of the Crosbie family. A lease from the Crosbie papers gives a precise account of what remained at that point: one chancel, one steeple, one cloister with various chambers built in lime and stone, two churchyards, and a water mill with its course of water.