The original foundation of Quin Abbey was very early, but the first church burned down in 1278AD and a Norman castle built on its ruins. The castle featured a large, round tower at each of its four corners, and the remains of these can still be seen.

In 1350AD, after the castle had been abandoned, the MacNamara's founded another Franciscan abbey, utilising the southern curtain wall of the fortress for the church's east-west axis. The cloisters were added in 1402AD, and the lady chapel and bell tower in 1430AD. Construction was of the abbey was completed around 1433AD.

The history of the abbey remained quiet until it was dissolved in in 1541AD, passing into the hands of Conor O'Brien, Earl of Thomond. He allowed the friars to remain at the monastery, but the building fell into a state of neglect, and by 1548AD it was described as "one great church, now ruinous, covered with slate, and a steeple greatly decayed".

O'Brien only held the abbey until 1584AD, at which time it was attacked by Donnchadh O’Brien. English troops were dispatched and reclaimed the abbey. Elizabeth I granted a pardon to Donnchadh, but the English nobles felt inclined to ignore it, being far from the throne and the threat of recrimination. They avenged themselves upon Donnchadh by hanging him from the back of a cart while they broke his bones with the back of an axe, then hanging him alive from the steeple of the abbey.

The English forces remained garrisoned at the abbey to prevent it from further attack, but were eventually driven out after the building was burned over their heads. Ownership returned to the MacNamaras, and the church was repaired, with the choir, lady chapel being re-roofed by 1604AD. A college was opened during this period, and 800 pupils enrolled - although it was remarked that the few remaining friars from earlier days were "old, helpless men with scarcely a memory of the pre-suppression friary".

In 1651AD, the abbey was sacked by the parliamentary forces of Oliver Cromwell, and the friars executed. In 1667AD, the abbey was briefly and half-heartedly restored. Several friars came and went up until 1681AD when the abbey was reported empty. However, there were again friars here by 1691AD when the cavalry of the defeated Irish army came to camp in the church grounds.

The friars presumably maintained some connection to the abbey for the following 80 years, as English Colonels are reported to have evicted them around 1760AD. One managed to remain living in the ruins though, and last friar of Quin Abbey, Fr. John Hogan of Drim, stayed there until his death in 1820AD.