What makes its position quietly arresting is the layering of history beneath and around it, a site that appears to have been continuously significant for worship and conflict across several centuries, with each iteration of the building displacing or erasing the one before.

The site was, according to the historian William Carrigan writing in 1905, the location of the ancient Catholic parish church of the Holy Cross of Castlecomer. References to this parish church appear in the Red Book of Ossory, a medieval ecclesiastical register, between the fourteenth and sixteenth centuries, suggesting a well-established place of worship long before the upheavals of the seventeenth century. The medieval church was most likely demolished when Christopher Wandesforde, an English planter, built a new church between 1635 and 1637 as part of his project to construct a planned town at Castlecomer. That church had a short and violent history. In 1641, Confederate Catholics attacking the town destroyed it; a number of Protestant planters had taken refuge inside the building when it was set alight, making its destruction both a military and a sectarian act. The present Church of Ireland structure, an eighteenth-century rebuilding, stands on or very close to this same ground, though the precise relationship between the current building and its medieval predecessor remains uncertain.

The church sits within the grounds of Castlecomer Demesne, reached by a path that climbs steeply from the entrance to the modern graveyard. The rise in ground level gives the building an elevated, slightly commanding position over the surrounding landscape, which itself hints at how deliberately chosen this spot has been across the generations.