Today there is no visible trace of it above ground. The town has simply swallowed it whole, and the streets and buildings of modern Fermoy were, in a quite literal sense, built from its bones. When the monastery was finally demolished in 1804, its stonework was broken up and used as construction material for the expanding town. What had been a medieval religious house became, stone by stone, somebody's wall.

The monastery was founded in 1170 by Donal Mor O'Brien, and it did not lead a quiet existence. In 1227 it was identified as the principal instigator of what became known as the Mellifont conspiracy, a serious revolt by Irish Cistercian houses, the order of monks who followed the austere rule associated with the Abbey of Cîteaux in Burgundy, against the authority of the wider Cistercian network and its efforts to impose continental discipline on Irish monasteries. Whether the Fermoy house was a ringleader by conviction or circumstance is not recorded. By the time of its dissolution in 1539 to 1541, most of its landed possessions were described as being waste, suggesting a community already in steep decline. After dissolution it lingered on as a parish church, though it was not remembered fondly in that role; one account described it as a mean Gothic building, which in the vocabulary of the period meant plain and undistinguished rather than cruel.

Two fragments appear to have survived the 1804 demolition. A pointed stone arch, possibly part of the original abbey fabric, was incorporated into a property boundary on the northern side of McCurtain Street, where it remains embedded in the urban landscape largely unannounced. A font believed to originate from the monastery was preserved and can be found in Fermoy's Church of Ireland church. Neither survival is dramatic, but together they suggest that the town, even as it dismantled the building, could not quite bring itself to discard everything.