The church walls at Quin are an extraordinary 2.8 metres thick in places, not because the friars built unusually robust stonework, but because they laid their monastery directly onto the scorched foundations of an Anglo-Norman castle, incorporating its rounded corner towers and curtain wall into the new structure without ever attempting to disguise the fact. The crossing tower of the friary sits precisely in line with the original castle gateway, and a small chamber within the wall, once the castle entrance passage, was simply walled off and fitted with an altar. Elsewhere, the SW corner of the church occupies what was the original corner of the keep. The result is a building that carries two quite distinct histories in the same stones.

The castle was begun in 1280 by Sir Thomas de Clare, one of the Anglo-Norman lords who had pushed into Thomond in the late thirteenth century. It did not last long. Around 1285 or 1287, Covea MacNamara stormed and burned it in revenge for the killing of a chief named O'Liddy, described in the sources as 'of the broad shield', and his brother. No attempt was ever made to rebuild it as a fortress. The site lay derelict until Síoda Cam Mac Conmara established an early religious house there in 1402, and then Maccon Mac Conmara, having secured a papal licence, formally founded a house for Franciscan friars in 1433. The friary was officially dissolved in 1541, but the friars continued to occupy it under the protection of the earls of Thomond and successive O'Brien landowners. When Donatus Mooney, provincial of the Irish Franciscan province, visited in 1616, he described Quin as 'a singularly beautiful pile of building, such as is seldom met with in monastic establishments.' The community was repeatedly expelled during the seventeenth century but kept returning, eventually relocating to a house at Drim, about two kilometres away. The last member of that community, Friar John Hogan, died in 1820 and was buried in the east ambulatory of the cloister at Quin.

The fabric of the friary survives to a remarkable degree. In the chancel, a sedilia, a recessed seat or tomb niche set into the wall for liturgical use, still bears traces of an early seventeenth-century stucco crucifixion scene that was more complete when the antiquary Thomas Dineley sketched it in 1681. The high altar remains in place beneath the triple-light east window. A holy water stoup in the nave, set into a ribbed vaulted recess, still draws modern votive offerings. Medieval graveslabs lie across the nave and chancel floors. The MacNamara founder's tomb occupies the northeast corner of the chancel, positioned so that it could function as an Easter Sepulchre, a temporary tomb used in the liturgical commemoration of Christ's burial and resurrection. Corbels in the west end of the nave are the only remaining evidence of a gallery that once gave guests staying in the west range a view down into the church below.