Nearby, the medieval masons left their personal marks on the same piers, small signatures cut into the fabric of a building they knew would outlast them. That it has done so is partly down to the extraordinary object the abbey was built to house: a fragment said to be from the True Cross, reputedly given around 1110 by Pope Paschal II to Muirchertach O'Brien, King of Munster. It was this relic that gave the place its name and its pulling power, drawing pilgrims across the medieval centuries and making the abbey one of the more significant religious foundations in Munster.

The abbey was founded in 1180, possibly on the site of an earlier Benedictine house established by Donal O'Brien, King of Limerick, in 1169, and a charter was granted by its founder Domhnall Ua Briain in 1185 to 1186. What visitors see today is the result of two distinct building campaigns. The earlier, late twelfth and early thirteenth-century work survives in the nave and its arcades, relatively plain in style and built in rubble masonry, with traces of the original lancet windows still legible in the west wall. The more lavish phase came in the fifteenth century, sponsored by the Earl of Ormonde, and transformed the east end of the church entirely. The monk's choir, transepts, chancel and crossing-tower all date to this period, executed in finely cut, closely jointed limestone. The decorated sedilia in the chancel, a set of recessed seats used by clergy during Mass, are traditionally called the Tomb of the Good Woman's Son and carry a series of heraldic shields, the largest displaying the royal arms of England alongside the Butler and FitzGerald arms. Between the two south transept chapels stands the structure known as the Waking Bier of the Monks, thought to have functioned as an elaborate shrine through which the True Cross relic could be viewed. In the north transept a rare survival catches the eye: a medieval hunting scene painted on plaster in red ochre, charcoal black, lime white, and vermilion. The abbey passed to Gerald, Earl of Ormond, in 1563, a short-lived Cistercian revival in the early to mid-seventeenth century was suppressed by Cromwellian forces, and the last professed monk from Holycross died in 1752.

The two bells now hanging in the crossing-tower were not original to the site. Both were found buried beneath the ruined parish church of Buolick, near Urlingford, and one was cast before 1250. The church itself was re-roofed between 1971 and 1975 as part of a broader reconstruction, which also involved a partial rebuilding of the cloister arcade to the south. The cloister walk is otherwise well preserved, and the east range retains a small chapterhouse, its doorway ornamented with an unusual billet moulding, a decorative pattern of small raised rectangular blocks. The abbot's quarters to the south-east were remodelled in the fifteenth century with evident attention to comfort, including fireplaces and projecting garderobes, the medieval equivalent of exterior latrines cantilevered from the wall.