The Franciscan friary here has been, at various points in its history, a military fort, a weaving factory, a Dissenter's chapel, and an army barracks. That a functioning friary occupies the site today is almost against the odds.

The friary was founded in 1269 by Otho de Grandison, and by the time of its Dissolution in 1540 it comprised a church, belfry, dormitory, hall, three chambers, a kitchen, a stable, a weir, and associated land. A north transept, sometimes called a Lady Chapel, was added in 1318. Cromwell's assault on Clonmel in 1650 badly damaged the buildings, and a military fort was promptly constructed on the site, destroying what remained of the cloister and domestic ranges, the covered walkways and living quarters that typically surrounded the central courtyard of a medieval friary. English weavers then set up a factory in the old fort towards the end of the 17th century. In 1705 the surviving chancel was repaired and given over to a Dissenting congregation, which used it until 1789, when the Franciscans recovered possession, only to lose the building again around 1813 when it became a barracks. The friars returned once more in 1828, and the church was substantially rebuilt in 1883, though that rebuild deliberately incorporated the north wall of the original 13th-century choir and the 15th-century tower.

The tower is the most revealing survival. Seven storeys of sandstone, roughly 2.7 metres by 3 metres in plan with walls a metre thick, it retains its original internal piers that once carried a vault, and a sandstone staircase that begins steeply and becomes spiral as it rises. The fifth floor is covered by a beehive vault whose wicker-centring, the temporary framework of woven rods used to shape the stone during construction, is still legible in the stonework. Some of what looks medieval on the exterior, including the crenellations and certain windows, was added later. Inside the church a double effigial Butler tomb survives; a 17th-century Franciscan recorded additional tombs of black marble commemorating the Prendergasts, Mandevilles, Walls, Whites, Brays, Moronys, and others, but by the early 20th century only the Butler tomb remained in place. Excavations in 1994 and 1995 behind the nearby Main Guard courthouse uncovered a wall pre-dating that 1670s building, almost certainly part of the Franciscan complex, and a burial ground connected with the friary was found some 50 metres to the north-west, apparently continuing in use after the Dissolution until the courthouse site was developed.