St. Mary's served as the church for the medieval (Norman) High Town, as Bishop David Rothe describes in the early 17th century.

[6] Throughout the Middle Ages, the church's upkeep was financed by the town's (later city's) merchants by collection of 4d.

At the time of the Confederation of Kilkenny (1642-1649), it was again in Catholic hands with Archbishop Rinuccini celebrating High Mass.

[12] Around 1560, the Rothe family (wealthy merchants) built a chantry chapel in the north transept of the church dedicated to the Archangel Michael.

Even after the reformation had seen the church turned over to Protestant worship, these chapels continued to be used by the Catholic congregation.

It is believed that the bell-tower was a separate building,[citation needed] today indicated by a concrete platform in the churchyard.

There is also a memorial plaque for his nephew in the church who was a founding member of the Kilkenny Archaeological Society.