Built by the Bishop of Killaloe, Donagh O'Kennedy of the O'Kennedy clan as a sort of two fingers to the Norman Butlers who had previously built an  Augustinian monastery at Tyone, it was built closer to the town in 1254, according to the Annals of Nenagh.

On 07/04/1324, the Franciscan Friars were ordered to cease segregation of the Friars as some of the Houses were composed of Friars of Irish descent while others were of English only. The order was they were to be mixed evenly within 10 days upon pain of excommunication. Likewise the same for those Friars who were designated readers as it was feared they were fomenting dissent.

(Ormond Deeds)

The Friary was the chief house of the Irish Franciscan friars and was important enough to have had a Provincial Synod held on the site in 1344. Reputedly it was also here that the Annals of Nenagh were written.

‘‘In 1344, a provincial chapter was held here, and one of its learned members completed an historical work of high character which is often quoted, called the ‘ Annals of Nenagh.'

(Dublin Saturday Magazine Issue 95)

The complex was destroyed during the reign of Elizabeth the 1st and subsequently rebuilt. It was finally suppressed during Cromwells campaign in Ireland.