Samuel Lewis, in A Topographical Dictionary of Ireland... (1837) writes that the MacCarthy's founded the friary in 1312. The friary's foundation has also been attributed to the Anglo-Norman de Barry family in the early 14th century. Though the friars were well established in Timoleague by 1320, the earliest surviving parts of the ruined friary date from later in the 14th century. It is likely that they were based in Timoleague Castle prior to the construction of the friary. By the 15th century, the friary was recognised as a centre of learning, and also as an important ecclesiastical centre. In 1460, Timoleague became one of the first houses in the Franciscan order to recognise the observantine reform. Tadhg Mac Cárthaigh, also known as "Blessed Thaddeus", is said to have been educated by the friars in Timoleague around this time. According to the Annals of Ulster, in 1505 Patrick Ó Feidhil, a famous preacher in Ireland and Scotland, was buried in the friary. An important patron of the church was Bishop John Edmond de Courcy, along with his nephew James, 8th Baron Kingsale. They funded the construction of the Gothic style bell tower, the infirmary, the library, and one of the dormitories. De Courcy had been a friar in Timoleague before being made a bishop. The tower was added between 1510 and 1518. They also contributed to the friary's collection of plate. John de Courcy was buried in the transept of the friary, but in the Cromwellian period his grave was desecrated and his bones thrown into the estuary. Despite the dissolution of the monasteries in 1540 by Henry VIII, the friars remained in Timoleague. In 1568, the friary was seized by crown forces, and in 1577 was granted to James de Barry, 4th Viscount Buttevant. Despite this, Timoleague remained an important centre for the training of the novitiate until the late 1580s. In 1590, the Protestant Bishop of Cork ordered materials to be taken from the friar's mill to be used in the construction of a new mill he was building, but the river flooded and swept away all progress on the new mill. In 1596, the friary's wooden cells were removed and were being transported by ship, but the ship sank in a storm. After the succession of James I, the friary was reclaimed by Catholics in 1603, and was repaired in its entirety by the end of 1604. During