No documentary evidence places a church or chapel inside the fort during the seventeenth century, yet a drawing made in 1685 by the military engineer Thomas Phillips tells a slightly different story. In it, a bellcote, the small wall-mounted frame used to hang a bell in place of a full tower, can be seen at the western end of a building that strongly suggests a place of worship. The structure is there, in ink, and yet officially it was not supposed to exist.

By the early eighteenth century the building had acquired memorials, the earliest dating to either 1703 or 1728, which places it firmly within the life of the garrison community that occupied the fort across that period. Duncannon Fort itself had been a significant defensive position on the western side of Waterford Harbour since the late sixteenth century, and a community of soldiers, officers, and their families would have had practical need of a chapel, whatever the formal record chose to acknowledge. The memorials suggest the building served that community across at least a generation, perhaps longer. None of this fabric survives today. The church has been entirely lost, leaving Phillips's drawing as the closest thing to a portrait of it.