The west gable and the western end of the north wall share a masonry style so close to that of the nearby church of Templedermot, just six metres to the south, that the two may have been built from stone quarried at the same source, or may even be contemporary. Scattered across the floor of the stone-vaulted sacristy, a small room off the north wall, are loose architectural fragments carved in the Romanesque manner, along with chevron-decorated pieces, all dating to the twelfth century. They lie there still, dislodged from wherever they once sat.

The priory was dedicated to St. Mary and adopted the rule of St. Augustine sometime after 1140, possibly following the Arrouasian observance, a reformed branch of the Augustinian order that spread through Ireland during the twelfth-century church reform movement. The monastery sat within a much older monastic cashel, a stone-walled enclosure of early medieval origin, and the Augustinian community inherited a site already dense with ecclesiastical buildings. In 1193, the monastery was attacked by Gilbert de Nangle, and it was argued as early as 1860 that the east end of the priory church was rebuilt in the aftermath. The fifteenth century brought a more ambitious expansion: a cloister garth (an enclosed garden), an ambulatory (a covered walkway around it), a stone-vaulted sacristy, a chapter house, and a probable refectory at first-floor level were all added to the north side of the church. Two thirteenth-century lancet windows of noticeably different styles were reset into the east gable during this phase, apparently removed from elsewhere in the building and inserted as a matched pair, in the process cutting across an earlier aumbry, a wall recess used to store liturgical vessels. A twelfth-century double piscina, a paired basin used for rinsing chalices during Mass, survives with the base of its central octagonal column still intact, though a later flat-headed aumbry was inserted into it during the same rebuilding work. In 1442, papal records name Hilarius O'Ferral, an Augustinian canon from Cloontuskert in Co. Roscommon, as the replacement prior, suggesting the community remained active and connected to wider church networks well into the late medieval period. The priory was suppressed around 1541, and by 1570 Thomas Philipps had been granted a twenty-one year lease of the island described simply as containing four dwellings and the stone walls of a monastery. A further lease was granted to Richard Power in 1590 on similar terms.

The island is accessible by boat from the Roscommon shore of Lough Ree, and the priory church is the largest of the six ruined buildings clustered on Inchcleraun. The Office of Public Works carried out consolidation and pointing work in 1908 and 1909, including the installation of stiles to keep cattle out of the larger church, and cleared ivy from all the churches in 1932 and 1933. Inside the sacristy, the Romanesque fragments on the ground reward close attention, as does the east gable where the two mismatched lancets, one with a roll and keel moulding, one with an external rebate, sit side by side in their fifteenth-century embrasures, quietly advertising the complicated history of the wall around them.