The church, built to a plan of nave with aisles and a chancel with transepts, stands very nearly complete, its walls rising to considerable height and its stonework telling the story of at least two distinct phases of construction spread across several centuries. Look closely at the masonry and the mixture becomes apparent: the dressed stone of the transepts and chancel, including the corner quoins, is Dundry limestone, a fine-grained oolite quarried near Bristol and shipped across the Irish Sea; sandstone appears on the western facade; and Old Red Sandstone alternates with Dundry on the voussoirs, the wedge-shaped arch-stones, of the north transept arch. This was an ambitious operation, and the church is dated architecturally to roughly 1210 to 1240.

The foundation's origins are somewhat convoluted. Hervey de Montmorency, who received the baronies of Shelburne and Bargy from Dermot Mac Murrough in 1170, made a grant of land in the early 1170s to the Cistercians of Buildwas Abbey in Shropshire. They never came. The grant passed instead to St Mary's Abbey in Dublin in 1182, and the resulting house, known as the Port of St Mary, was consecrated in 1201 by Herlwyn, bishop of Leighlin and a nephew of Hervey himself, who had likely pushed the building work forward. The community had a turbulent reputation in the fourteenth century, its monks described as violent and rebellious, yet the abbey's possessions remained largely intact until the Suppression in 1536. In 1545 the crown granted the abbey and its lands to Sir Osborne Etchingham, who converted part of the monastic complex into a dwelling, inserting domestic fireplaces and rectangular windows into spaces that had once served as chapels and dormitory passages. That makeshift residence may have been abandoned once a more conventional house was built about 300 metres away in the early seventeenth century. The estate passed by marriage to Sir Arthur Chichester in 1650 and remained with that family well into the twentieth century. Conservation work began under Lord Templemore in 1858 and continued after the abbey was placed in state guardianship in 1895.

The most curious structural detail is the fortification carried out in the fifteenth century, when a tower was added over the crossing, the central junction of nave and transepts. This required thickening the piers and blocking the nave arches nearest the crossing, so that the earlier and later arches now sit side by side with visibly different profiles and pitches. The tower's upper chamber, reached by stairs built into the thickness of the walls, has cusped ogee-headed windows on each face and seven rope-holes through its vault, suggesting it served as a belfry. The wall-walk at the top of the east wall stands roughly 25.6 metres above the ground. Elsewhere in the ruins the refectory walls survive nearly to their full height, a reader's lectern niche still visible in the south wall, and the foundations of a lavabo, a circular washing basin used by monks before meals, were uncovered near the south-west corner of the cloister.