The Priory of the Holy Cross has left almost nothing visible above ground, yet its stones are, quite literally, still there, pressed under the town that consumed them. A writer in around 1682 recorded that the friary had been "totally defaced by Cromwell's army" around 1652 and its stones used to build houses and fortifications, adding that "the footsteps of the ancient friary in this town are at present not discernible." By 1756, only some vaults remained; by 1758, a single arched building, thought to be the Desmond burial chapel, was the sole visible remnant. Today, even that is gone.

The priory was founded in 1243 by John Fitz Thomas FitzGerald, who was himself buried there in 1261 alongside his son Maurice, both killed at the Battle of Callan. It became the preferred burial ground of the FitzGerald lords and earls of Desmond, the dominant magnate family of late medieval Munster. Maurice, the 1st earl of Desmond, who died in 1356, was interred here, as was Thomas, the 8th earl, who died in 1468. One scholar, writing in 1854, counted three lords of Desmond and seven earls among those said to be buried within its walls. The priory's history was not purely one of solemn ceremony. In 1295 a man named Nicholas Strange was charged with stealing silver and wheat from the complex. In 1325 Diarmait Mac Carthaig, king of Desmond, was killed inside the priory itself by Nicholas FitzMaurice or his son William. By 1580, with the Desmond rebellion in full collapse, the Lord Justice Sir William Pelham garrisoned the building with 300 footmen and a company of horse, apparently because it was the only suitable structure the retreating earl had not already destroyed. Four years later a government survey described it as ruinous. The priory was granted to Edward Denny in 1587, and the process of dissolution, already well advanced, became irreversible.

The priory's original position was on the River Gyle, a waterway now entirely covered over by Ashe Street, the Mall, Bridge Street, and several other central thoroughfares. Historians have suggested that Tralee's main square occupies the area where the cloisters once stood, though the documentary evidence does not allow for certainty. What archaeological work has established is that significant material survives below street level. Excavations in 1997 at the Abbey carpark by Martin E. Byrne uncovered in situ human skeletal remains and a substantial stone wall roughly 860mm wide, buried about a metre below the present ground surface. The following year, Laurence Dunne excavated nearby at Lower Abbey Street and found another wall, approximately 1.2 metres wide, constructed of unhewn limestone set in clay without mortar, with layers of bone and charcoal accumulated above it. The priory has not disappeared; it has simply gone underground, waiting beneath the ordinary business of a modern town.