The old burial ground at Ballyduff contains 108 unnamed grave markers, twenty-three tombs with no identifying plaque, and lintelled graves, stone-covered burial chambers laid horizontally over the dead, several of which are now open or collapsed. What makes the place particularly striking is not the scale of its ruin but the way the vanished church has been absorbed into it: dressed stones from the medieval building have been pulled out and reused as tomb construction material, grave markers, and headstones, so that the architecture of worship has become, almost literally, the furniture of burial. One fifteenth-century ogee window head, a carved arch with a characteristic double-curved profile, now serves as a gravemarker on the east side of the old burial ground. A complete holy water stoup, of the projecting basin type, has been repurposed as a burial marker elsewhere in the same section.

The church itself had a troubled later history before it disappeared entirely. In 1615, a Royal Visitation recorded the parsonage of Balliduff as a gift of Sir Richard Boyle, the powerful English colonist who became Earl of Cork, but noted it was 'waste and worth nothing'. The church was still listed among the parochial churches of the diocese in 1622, and remains of the building were reportedly visible in the graveyard around 1837. By 1841, however, no trace of any features remained. A graveyard survey carried out by Laurence Dunne in 2010 found only two named tombs in the old medieval section: one partially legible as Moynihan, the other bearing simply the inscription O'Connor, Kilcummin Beg. Both are of the strong-box type, a raised rectangular enclosure of mortared stone, and both are in poor condition. A concentration of unmarked stones at the extreme northern corner of the old burial ground may indicate a famine burial area, though this has not been confirmed through excavation.

The old and new sections of the graveyard are separated by a low rubble wall of local sandstone, capped with upright stones set on edge in the manner known as soldiers. Access into the medieval section is via a step-stile, or through a ragged gap at the western end of the dividing wall, which Dunne's survey notes is difficult and uneven underfoot. The new section, opened around the early 1950s, sits to the south and is in considerably better order than its neighbour, where virtually every one of the twenty-five recorded tombs is in some state of collapse or dilapidation.