That turned out to be wrong. Research published in 1990 established that the connection to the Cistercians was entirely spurious, and that the site was in fact an Augustinian foundation, its origins lying in a grant of land made in 1189 by King Donal Mór O'Brien to the Augustinian canons at Clareabbey. The correction matters, because it quietly repositions the ruin within a different network of medieval monasticism, one that stretched across Clare and left its own distinct architectural and documentary traces. The church still stands on a low but noticeable rise in rolling pasture and marshy scrub, its limestone walls reaching their original height, the gables climbing to an estimated seven metres.

The site's origins are traditionally traced to the 7th-century St Cuana, tentatively identified by the antiquary T.J. Westropp with Mochonna of Feakle and Kilquane. By the early 14th century the church was valued at 26 shillings and 8 pence in the Ecclesiastical Taxation lists of 1302 to 1307, and in 1273 its abbot, Florence O'Tighearnaigh, had risen to become Bishop of Kilfenora. At the dissolution of the monasteries the property passed to Murrough O'Brien, first Earl of Thomond, and remained in O'Brien hands through subsequent generations. A 1621 grant made by Dermot O'Brien, 5th Baron Inchiquin, describes not just the church but 'the abbey and cloister of Kilshanny, with the old ruinous walls sometimes called the abbot's house and the precincts and circuit of the abbey,' confirming that a fuller monastic complex survived, at least in fragmentary form, into the early 17th century. The church itself is dedicated to Our Lady and St Augustine.

The fabric of the building repays close attention. The rectangular nave, built of randomly coursed limestone rubble with dressed quoins at the corners, contains three doorways, two windows in the south wall, and a three-light switch-line tracery window in the east gable, its hood moulding still intact though the sill is broken. In the north wall, a wide shallow recess shelters an early 18th-century Thynne family chest tomb, and two small aumbries, niches used for storing liturgical vessels, survive in the east and south walls. Beneath the east window the remains of a stone altar are still visible. Westropp noted in 1900 that the graveyard contained far more architectural fragments, shafts and window-heads, than the church itself could account for, pointing to the wider cloister buildings whose wall footings continue to turn up during grave digging. About 170 metres to the north-east lies St Augustine's Well, a further trace of the monastic landscape that once extended well beyond what the standing walls now suggest.