Its crow-stepped parapets and corner pinnacles date only to around 1827, when it was built with assistance from the Board of First Fruits, a body that funded Protestant church construction across Ireland in the eighteenth and early nineteenth centuries. But beneath it, and beneath the graveyard itself, lies a much older sequence of occupation that stretches back at least to the early fourteenth century, and possibly further. The medieval church it replaced was dedicated not to St Owen, as the current ruin is, but to St Mary, and at some point that dedication quietly changed, the reasons now lost.

The place was once known as Loughsewdy, or Loxeuedi in its medieval Latin form, and the church attached to that settlement had a notably complicated history. The 1306 ecclesiastical taxation of Ireland valued it at 40 marks yearly, and throughout the fifteenth century papal records refer to the resignation and appointment of its rectors by name, among them John Ochaynean in 1428 and a John Macmurchertaid in 1440. In 1538 the parish was united to the bishopric of Meath, and in 1545 Henry VIII selected it to serve as the new cathedral church of that diocese. Whether it ever functioned in that capacity is not known, but the nomination alone suggests it was a building of some standing. By the mid-seventeenth century it was a ruin. Bishop Anthony Dopping and his parishioners subsequently rebuilt the chancel, though his own visitation book of 1682 to 1685 noted that the chancel stones had been taken during the Cromwellian period to construct Loxeudy Castle nearby. In 1691, the soldier and chronicler George Story described the church as standing on a rise close to what was nearly an island, surrounded on three sides by a lough and bounded to the northwest by bog, connected to the land only by a narrow neck to the southwest. A sketch he made that year, showing the church alongside the Athlone road, a cluster of houses, and the Fort of Ballymore, survives as one of the few visual records of the site at that period.

The graveyard still holds traces of the longer story. Twenty-five metres east of the church ruins stands a small early seventeenth-century mortuary chapel or mausoleum, a low structure used for the burial of a family or individual of local importance. In 1980 a fragment of an ogee-headed window, a style associated with late medieval ecclesiastical architecture, was found lying on the surface of a grave near the mortuary chapel; it almost certainly belonged to the medieval church of St Mary, though its precise location within the graveyard has since been lost.