Yet the place is also a working graveyard, four centuries of local burials layered through the nave and chancel and surrounding ranges, so that medieval stonework and nineteenth-century headstones occupy the same space without much ceremony. Sixteenth and seventeenth-century sources describe the wider precinct as having included grist mills, water mills, eel weirs on the nearby River Bride, gardens, and houses, none of which are visible today; a geophysical survey carried out by the Discovery Programme in 2015 found little trace of them, most likely because they were built in timber.

The friary was founded in 1465 by Cormac Láidir MacCarthy, 6th Lord of Muskerry, on land he had recovered from the Anglo-Norman Barret family around 1420, territory that had originally formed part of the medieval kingdom of Desmond. He established it for the Observant Franciscans, a reformed branch of the order with stricter rules on poverty, and the buildings were laid out as a single planned complex rather than accumulated piecemeal. Metrological analysis of the plan suggests it was carefully designed before construction began. The church follows the pattern typical of late medieval Irish mendicant friaries, with an aisled nave and a chapel in place of a true transept, the latter arrangement possibly influenced by Timoleague Franciscan friary in west Cork, whose patrons were the MacCarthy Reagh, a junior branch of the same family. Cormac's own story ended badly: in 1495 he was killed by his brother Eoghan and Eoghan's sons, and buried here in a Franciscan habit. His probable tomb recess sits at the east end of the chancel's north wall, the most privileged position in a friary church, traditionally reserved for the founder. The friary survived official suppression in 1542 through MacCarthy patronage, was sacked in 1584 and again around 1590, repaired in 1603 and the 1620s, and only finally abandoned during the Cromwellian period. A seventeenth-century Franciscan historian, Donatus Mooney, recorded that a gold-and-silver rood cross once hung from the tower inside the church before English soldiers destroyed it in 1584.

The tower, around 24 metres high, is one of the more distinctive features still standing. Its internal circulation is elaborate, with spiral stairs, mural passages through the walls, and a lintelled passage at ground level running beneath it. Among the gravestones spread through the nave is the tomb of Art Ó Laoghaire, killed in 1773 after a feud with Abraham Morris, High Sheriff of County Cork. His wife, Eibhlín Dubh Ní Chonaill, an aunt of Daniel O'Connell, composed the lament Caoineadh Airt Uí Laoghaire in Irish in his memory, a poem that gained wide recognition during the twentieth century. The friary is approached from the road to the west by an embanked avenue, and the cloister arcade is the only significant part of the complex that has not survived.