The east gable of the abbey's chancel contains what appears to be a robbed opening, and some authorities have argued that this was the original home of the Romanesque window currently installed in the nearby structure known as the cathedral. Whether or not that theory holds, the implication is striking: that decorative stonework of considerable age has been moved between buildings on the same complex, leaving a gap where something beautiful once was.

The abbey at Annaghdown, on the shores of Lough Corrib, was founded sometime after 1195, when it was granted to the Canons Regular of St Augustine, a religious order following the Rule of St Augustine that became widespread across Ireland and Britain in the twelfth century. The church is described as being of at least three distinct building phases. Its earliest surviving section is the chancel, which dates to the Transitional period, that stylistic moment in the late twelfth and early thirteenth centuries when Romanesque rounded forms were beginning to give way to Gothic pointed ones. The chancel retains two finely cut opposing round-headed windows in its side walls, the southern example carrying Romanesque decorative carving on its arch terminals. Later additions include a pointed arch doorway in the north wall of the nave, a trefoil-headed window nearby, and a rectangular window in the west gable. The nave itself, now restored, runs twenty-six and a half metres east to west. South of the church lie the remains of a cloister, a covered walkway surrounding an open court that formed the organisational heart of monastic life, though here only the foundations survive. The domestic ranges to the east, south, and west are in varying states of ruin: the east range was once two storeys high, divided on the ground floor into five rooms with doorways opening onto the cloister; the south range is largely featureless but preserves fragments of a Romanesque chancel arch set into a recess in its southwest corner; and the west range has been reduced to a single fortress-like wall pierced by small rectangular windows. A cross-slab, a carved stone marker of early medieval type, is also associated with the site.

The complex sits 150 metres south-southwest of a second ruined structure known locally as the Nunnery, making Annaghdown an unusually concentrated cluster of medieval ecclesiastical remains on a single stretch of shoreline. Visitors who look carefully at the stonework across the different buildings will find the shifting architectural vocabularies of several centuries compressed into a relatively small area.