That distinction was stripped away at the Synod of Rathbreasail, the great reforming council that reorganised the Irish church, and transferred to Ardfert. The building that survives is older than that moment of ecclesiastical politics, and stranger. Its walls are built not from the limestone that lies underfoot in the surrounding district but from Old Red Sandstone hauled from a considerable distance, a deliberate choice whose reasoning is now lost. The masonry is of a type nineteenth-century antiquarians called cyclopean, meaning the stones are massive, undressed, and fitted with a precision that dispenses with the need for small infill. In the west doorway, single stones run through the entire thickness of the wall.

The western portion of the church is thought to date from a rebuilding associated with Abbot Cormac O Killeen, who died in 969, and the nave has been dated by scholars to the tenth or eleventh century. The east window attracted particular attention from early antiquarians. Writing in 1845, George Petrie noted that it was unusually large for an Irish church of its period, measuring roughly a metre in external height and just over a metre in external depth, and that its architrave moulding was matched by a similar treatment on the doorway. Richard Rolt Brash, writing in 1875, regarded it as among the earliest Irish examples of decorative moulding applied to window openings, with jambs and sills finished in an arris moulding, a narrow sharp-edged ridge carved along the stone angle. He compared it to a window at Clonmacnoise. The east end, with its semicircular-headed window and Romanesque chancel, appears to be a later addition to an already ancient nave. The antae, projecting flat pilasters at each gable corner, are a characteristic feature of early Irish mortared stone churches.

The church also acquired a footnote in post-Reformation local history. Samuel Morris of Ballybeggan, who died around 1700 and whose family owned much of the surrounding land, left instructions in his will directing his son to repair Ratass. He called on his neighbour Colonel Edward Denny of Tralee Castle to assist, noting that he himself had helped repair the church at Tralee. He added a conditional clause, specifying that the repair should proceed only if the Act of Settlement were not repealed within twenty years, a hedge against the possibility that the return of the Stuarts might make the maintenance of Protestant churches pointless. By 1906 the interior was filled entirely with vaults and graves, the old west doorway had been bricked up, and a headstone had been set into the masonry where the opening once stood.