The Franciscans arrived around 1240 on what was then a small island in the River Fergus, and the settlement that accumulated outside their walls eventually became the county town of Clare. That urban origin gives the ruins an unusual quality: they sit not in a field or on a hillside but folded into the fabric of a busy modern town, their walls still standing to their original height of around ten metres, the gables reaching fifteen.

The earliest buildings were probably timber and temporary, but the political landscape shifted decisively in 1270 when the Anglo-Normans were defeated at Clare Castle. Toirrdelach Mór Ó Briain of Clonroad used the opportunity to commission a permanent stone church in the Gothic style, with a long nave and chancel terminating in a five-light lancet window in the east gable, still standing at roughly eleven metres high. Construction continued well into the following century; Matha Caoch MacNamara added the refectory and sacristy in 1349. A fifteenth-century phase of rebuilding brought a cloister garth to the north around 1470, a southern transept, and a four-storey crossing-tower inserted between the nave and chancel. That tower was partly rebuilt in the eighteenth century, when crenellations and corner pinnacles were added, giving it a slightly composite appearance. The friary was dissolved in 1543, though the friars remained until 1570. It then served, with a certain grim versatility, as a law court and a prison before being adapted for Protestant worship following a royal visitation in 1615. A gateway known in the eighteenth century as the great gate of the abbey of St Francis sealed the complex from the town around it, visible on Hewett's map of 1736. The church closed in 1871, the ruins were returned to the Franciscan Order in 1969, and between 2011 and 2012 the Office of Public Works re-roofed the nave and glazed the windows.

What makes a close visit rewarding is the density of detail that survives at eye level. A carved figure of St Francis occupies a niche on a pier of the crossing-tower, showing the stigmata on his side, hands, and feet. A screen of flamboyant tracery beneath the same tower may originally have formed part of an elaborate tomb. On the arch between the nave and the southern transept, known variously as the Lady Chapel or the Michael Chapel, there is a carved image described as Christ's Pity or Ecce Homo, the hands bound and the instruments of the crucifixion arranged around the figure. Sedilia, the recessed stone seats built into walls for clergy during services, line the nave; most are damaged or partially blocked by later memorials. The tombs of several Clare families, among them the Inchiquins, the MacNamaras, the Considines, and the Woulfes, are embedded throughout the walls, some carved, some inscribed, accumulating across four centuries of local burial practice inside a building that had already changed hands more than once.