The complex sits on what was formerly an island, with the Kings River running along its northern edge and a secondary channel defining the south. Within that watery boundary, the site grew over three centuries into something closer to a fortified settlement than a conventional monastery. The later walled enclosure, dating to between 1450 and 1475, functioned as a bawn, an enclosed defensive yard designed to shelter tenants and cattle in times of trouble, and its turreted walls still stand to a considerable height. A 15th-century Latin document refers to it as the "villa prioris", the prior's town, explicitly distinguished from the adjacent medieval town of Kells some 400 metres to the east. That a community of Augustinian canons should have needed, and built, what amounts to a small fortified precinct tells you something about the conditions of life in medieval Kilkenny.

The foundation was established in the late 12th century, most likely around 1193, when Geoffrey fitz Robert received a land grant from William Marshal, who had only come into possession of Leinster the previous year. Fitz Robert had earlier set up a small collegiate church on the site dedicated to St Kieran of Sighir, an early medieval saint, before importing four Augustinian canons from Bodmin Priory in Cornwall. One of those canons, Hugh de Rous, became prior and later the first Anglo-Norman bishop of Ossory in 1202; he was buried in the chancel, which had been completed before 1218. The priory's history across the following three centuries lurches between construction and catastrophe. The town of Kells was burnt by William de Bermingham in 1252, the region was devastated by the Bruce invasion of 1317, and the Fitzgeralds of Desmond sacked Kells again in 1327. Local families, particularly the Lahys, Tobins, and Whites, became deeply enmeshed in the priory's governance, not always through legitimate channels. Nicholas White held the priorship without proper authority from around 1446 to 1469, successfully resisting a challenge backed by papal support from the bishop of Emly. His successor Edmund Stapleton wrote to the pope in 1471 to report that divine worship at the priory had been neglected. It dissolved in 1540, its lands passing to James, Earl of Ormond, and later to Margaret Fitzgerald, countess of Ormond, whose name appears as proprietor on the Down Survey barony map of 1655 to 1656.

The surviving fabric rewards close attention. The church was originally cruciform, with early Gothic arched openings in dressed sandstone, and the archway to the south transept remains its best-preserved early feature. Fragments of painted plaster recovered during excavations by Thomas Fanning in the 1970s and Miriam Clyne in 1996 revealed that the interior walls once carried a false ashlar pattern in red paint, with traces of deep red, black, and orange decoration in the chancel and transept; two tomb niches were painted orange and may once have contained painted figures. The chancel's limestone columns carry capitals carved with botanical motifs closely comparable to those at the medieval church at Gowran, dated to around 1260 to 1275. The roof had been covered in slate and finished with green-glazed ceramic ridge tiles, a detail easy to overlook but suggestive of considerable ambition for what began as a modest island foundation.