During groundworks for the centre's construction in 2005, archaeologist Cóilín Ó Drisceoil identified what turned out to be a mass burial ground, prompting a full excavation the following year led by Brenda O'Meara. What emerged was not a scattered or improvised field of the dead, but a densely organised cemetery that had been in use for just three years, between 1847 and 1850, and had been forgotten entirely beneath the city.

The burial ground occupied the south-eastern corner of the former Kilkenny Union Workhouse, established in 1843, in an area of open ground outside the women's yard. Sixty-three subrectangular pits were excavated, and human skeletal remains were recovered from all but one of them, representing a total of 970 individuals. Each pit held between nine and twenty-five people, laid out in rows of three or four and stacked four to six bodies deep. Despite the scale and urgency of the burials, almost every individual had been placed in a coffin, fragments of wood and iron nails surviving in many cases. The near-uniform orientation, with heads to the south-west and feet to the north-east in all but four instances, suggests a degree of organisation and care even under extreme pressure. The soil backfilling the pits contained lime and sulphur, both used historically as disinfectants, reflecting the cause of death: the workhouse had become fatally overcrowded, and typhus, scurvy, and other diseases moved rapidly through the population. Personal items recovered with some of the dead included textile pouches holding rosaries, copper finger rings, and religious medals. The excavation also revealed an entirely separate find cutting across the site: a cremation deposit of probable Bronze Age date, truncated by one of the nineteenth-century pits, a reminder that this ground had meant something to people long before the workhouse ever existed.