What makes the building quietly odd is a structural detail visible only on close inspection: although the nave and chancel are the same length on the inside, the outer courses of the nave walls extend beyond those of the chancel by up to two metres on the north side. The nave was evidently built after the chancel and wrapped around it, creating an illusion of normal proportions from the outside while the interior dimensions tell a different story.

At the Suppression of the Monasteries in 1541, the church was recorded as a possession of St Selskar's Abbey in Wexford town. It has been suggested, by Culleton in 1968, that the dedication was to St Margaret of Scotland, the eleventh-century queen later canonised for her piety and her reforming influence on the Scottish church. That identification remains uncertain, however, since no pattern, the traditional local feast-day gathering associated with a patron saint, has been recorded for this site. The chancel is the older part of the structure, and its east gable survives almost intact. A pointed chancel arch, roughly 2.1 metres high, opens into that section, where a pointed east window retains fragments of tracery and an external hood moulding finished with a carved head as a stop. Three areas of collapse in the chancel's side walls may mark where windows once were. The graveyard enclosure, a roughly rectangular space defined by masonry walls between 1.5 and 2.3 metres high, contains very few headstones, which gives the whole site an unusually spare, stripped quality. Approximately 300 metres to the south-south-east lies St Margaret's Well, a holy well, that is a natural spring traditionally associated with a saint and often the focus of local veneration, which shares the dedication and suggests the area carried some older significance before the church itself was built.