In 1311, two people broke into this church through a smashed window and made off with silver, textiles, and foodstuffs that various individuals had apparently been storing inside locked chests. The brazenness of the act suggests the building was already functioning as something of a community strongroom, which is an unusual role for a parish church and one that hints at the complex social life of a medieval Irish town. The church sits in a graveyard to the east of the old town of Athy, positioned just outside the medieval boundary, a placement that was common for early foundations and often reflects their origins predating any formal town plan.

The dedication to St Michael first appears in records from 1297 or 1298, and is thought to reflect the influence of the de St Michael family, Lords of Athy, who were most likely its founders. By 1569, the rectory was recorded as having formerly belonged to the hospital of St John, suggesting the church had passed through several institutional hands over the centuries. Both the Royal Visitation of Dublin in 1615 and Archbishop Bulkeley's visitation of 1630 found it in good repair, with the later visit counting 150 people attending divine service, a reasonable congregation for the period. Subscriptions for repairs were still being collected as late as 1677.

What survives today is a rectangular limestone rubble structure, roughly 27.8 metres east to west and 9.8 metres north to south, draped in ivy. The original entrance was a round-arched doorway in the south wall, later blocked, probably in the fifteenth century, when a smaller arch was inserted and a second doorway was added in the north wall opposite. The west gable, 1.2 metres thick, still stands to its full height and contains two square-headed windows stacked one above the other, an arrangement that points to the former existence of a loft inside. The east gable has been reduced almost entirely to foundation level. A font is said to have been buried somewhere within the church. Two thirteenth-century grave slabs and a sixteenth or seventeenth-century crucifixion plaque that once belonged to the building have since been moved to the Athy Heritage Centre and Museum on Emily Square, where they can be examined at closer range.