It is one of several violent episodes folded into the history of this site beside Ballylongford Creek, and it gives the ruin a quality that goes beyond the merely atmospheric.

The friary is thought to occupy ground that was already sacred, believed to have been the site of an earlier church dedicated to St Lachtin of Muskerry, Co. Cork, who died in 622 AD. A tenth-century reliquary hand associated with him, known locally as the hand of St Lachtin, is now held in the National Museum in Dublin, and the veneration attached to it suggests the site held significance long before any Franciscan arrived. The friary itself was begun around 1470 by John O'Connor Kerry, for friars following the strict Observantine Rule, a reforming branch of the Franciscan order that emphasised austerity. Pope Sixtus IV granted permission in May 1477 to house the friars, though the necessary mandate did not reach the prior of Ballinskelligs, who had to issue the actual licence, until 1478. The architecture reflects careful ambition: the choir's east window, divided into four lights by stone mullions and surmounted by bar tracery, rises to nearly four metres, and the triple sedilia recessed into the south wall of the choir, stone seats used by ministers during Mass, are so closely matched to examples at Adare and Askeaton in Co. Limerick that the architectural historian Leask, writing in 1960, suggested they may have come from the same mason. A processional cross found in a nearby field in 1871 carries a Gothic inscription dated 1479, naming Cornelius, son of John O'Connor, and Eibhlín, daughter of the Knight, as its commissioners; since John O'Connor Kerry had died in 1478, the cross was likely a gift to the friary from his son. The abbey was destroyed in April 1580, following the fall of nearby Carrigafoyle Castle, and three elderly friars, Fathers Donatus O'Hanrahan, Philip O'Shea and Maurice O'Scallan, were killed before the high altar. It lay empty until 1629, endured the Cromwellian raid in 1652, and yet guardians are recorded there until 1860, the last being a John Tuomy, though exactly when the Franciscans finally left is not known.