Visitors reached it by passing through a range of houses, turning down a narrow lane, crossing chapel grounds, and then descending a flight of seven steps to arrive at the door of the north transept. The floor inside sat seven feet below street level, which meant that flooding from the nearby river occasionally interrupted services altogether. This was Catholic worship during the Penal era, conducted in a low, T-shaped building that, as a contemporary description put it, made no pretensions to architecture.

The origins of the chapel reach back to the aftermath of the Dissolution of the Monasteries, when the Franciscans had managed to remain in Clonmel even after their monastery was formally suppressed. Following the Restoration of Charles II in 1660, they established a thatched chapel on the site. A letter written in 1712 by one Edward Tyrell, reporting on Roman Catholic activities in the town, refers to a "Mass house without the West gate," and the building appears on a late eighteenth-century map of Clonmel. By 1714 it had already been enlarged and reroofed in slate. Despite those improvements, the structure remained deliberately unassuming, its three internal galleries reached by stone steps on the outside of the building and its interior lit by long circular leaded windows. The sunken floor, the concealed entrance, the absence of any architectural ambition visible from the street: all of these were characteristic of penal-era Catholic buildings, constructed at a time when public worship was legally constrained and visibility was a liability.

The old church continued in use until around 1850, when it was demolished and replaced by the present Church of the Assumption, which stands immediately to its east. Nothing of the earlier building survives above ground, but the contrast between the two structures, one buried and hidden, the other a confident mid-Victorian presence on the streetscape, reflects a wider shift in the legal and social position of Catholic worship in Ireland across those intervening two centuries.