Clonfert's story begins with Saint Brendan in 577AD. Brendan was an indefatigable traveller, who had been at sea for years at a time, and who had founded other monasteries in Britain and Ireland before he came to this part of Galway. Clúain Fearta, the 'meadow of the miracles' would be his chosen resting place at the end of his days.

Brendan was a celebrated personality, who inspired others to dedicate themselves to religious life. His renown as a holy man and traveller was very attractive from the start, so Clonfert soon became a famous school of sanctity and learning. The monastery at would, like other monasteries, have begun modestly, with wattle cells for the brethren, surrounded by an earthen wall. Surrounded by bog land on the eastern edge of Co Galway, it had an island location, and drew to itself many men who wanted to renounce the world. At its height, Clonfert had three thousand monks.

     Clonfert was chosen as the centre of a diocese at the Synod of Rath Breasil in 1111, and this was reaffirmed at the Synod of Kells-Mellifont in 1152, when Clonfert was made a suffragen see of the new Archdiocese of Tuam. In 1175, Abbot Concors was one of three plenipotentiaries sent by King Roderick O'Connor to conclude the Treaty of Windsor. By this treaty, Roderick renounced forever the sceptre and kingdom of Ireland.

During the twelfth century, an Augustinian priory was founded at Clonfert, called St Mary's de Porto Puro. Its foundation was undertaken by Turlough O'Connor, in response to Saint Malachy's campaign of foundation and reform.

     Petrus O Mordha, the first Cistercian abbot of Boyle, became Bishop of Clonfert in 1152, and a chapter was formed. It was he who undertook the building of the great stone cathedral of Clonfert in 1167, under the patronage of O'Kelly, king of the Uí Muine territory. O Mordha drowned in the Shannon in 1172, on his way to the Synod of Cashel.

In the thirteenth century, Clonfert was confirmed to Arroasian nuns at the Abbey of Kilcreevanty. The convent was situated four hundred metres south of the cathedral. Separate houses of canons and nuns lived here over the next few hundred years.

     Like other religious houses, Clonfert suffered attacks. Being on the highway of the river Shannon, it was subject to ravages by the Danes and Irish chieftains. It was a richly endowed foundation, paying more to the Papal treasury than the Archdiocese of Tuam. It was unsurprising that it should have proved such a temptation to lawless blackguards. William de Burgo was among the guilty early in the thirteenth century.

Later that century in 1266, an Italian named John, was appointed bishop of Clonfert, and also Papal Nuncio. He collected crusaders tax on the authorisation of Pope John XXI. Bishop John is remembered as a great benefactor of his cathedral church, who did much to renovate and decorate with statuary the beautiful building.