Somewhere beneath or immediately around the present Franciscan priory in Waterford City lies the largely forgotten footprint of a medieval parish church known as St Mary's, or Our Lady's, a building whose appearance we can only partly reconstruct through the work of two cartographers separated by thirteen years. A map of 1672, later reproduced in Ryland's 1824 history of Waterford, shows a church with a spire positioned between its nave and chancel, giving it an unusual silhouette for an Irish parish church of that period. By 1685, when the military engineer Thomas Phillips surveyed the city, the same site appears to have been reduced, at least on paper, to a small rectangular structure, with no trace of that spire. Whether the building had changed, collapsed in part, or simply been drawn with less care is not recorded.

Documentary references to St Mary's go back to 1468, though the historical record thins out almost immediately after that earliest mention. Three grave-covers dating from the sixteenth and seventeenth centuries are associated with the site, flat carved slabs of the kind commonly placed directly over burials in late medieval Irish churches and graveyards. They survive as physical reminders that this was an active place of worship and burial long before the Franciscans established their presence there. The Franciscan priory that now occupies the ground is itself a continuation of a long tradition of religious use on the same urban plot, even if the institutional identity of what came before has been largely absorbed into the later foundation.