Carved with unusually elaborate decoration, it also retains a holy water font cut directly into its north jamb, a detail that speaks to the practical daily rhythms of monastic life. Inside, traces of a rood screen, the timber or stone partition that once divided the lay congregation from the choir monks, survive to the west of a 17th-century wall that was itself inserted to divide the nave from the chancel. The chancel's east gable is filled by a reconstructed traceried window from the 15th century, which replaced an earlier 13th-century arrangement of multiple lancet windows, small fragments of which still remain. The whole structure layers several centuries of construction and adaptation on top of one another in ways that become more legible the longer you look.

The O'Kelly family founded a house of Augustinian canons here sometime after 1140, on a site that had already served as an early monastery. The community was dedicated to St Mary, and the church that survives, comprising a nave and chancel each roughly 16 metres long and 8 metres wide, along with a 16th-century transept at the northwest end, represents building phases spread across the 13th to 16th centuries. Excavations carried out in 1971 and 1972 revealed the foundations of several earlier structures tucked beneath and around the standing remains, including a rectangular building at the northeast corner of the transept that archaeologists suggested could be a 15th-century chapel or possibly an Early Christian church predating the Augustinian foundation entirely. To the south of the church, within the modern graveyard wall, the domestic ranges of the priory once surrounded a central cloister. Most of this has been reduced to foundations, though a substantial section of the east range still stands to some height. Originally two storeys, it was significantly reworked in the 17th century, when an oven, fireplaces, and a chimney were inserted, suggesting the buildings remained in practical use well after the community itself had dispersed.

The wider landscape around the abbey carries its own quiet accumulations of history. A wayside cross lies to the south-southwest and a holy well to the south-southeast. To the northeast runs a togher, a raised trackway built across boggy ground, which local tradition holds once connected the priory to a medieval parish church. Whether that connection is literal or simply remembered, the togher is a reminder that Clontuskert was never an isolated retreat but a working institution embedded in a web of routes, landmarks, and neighbouring communities.