Murrough O'Brien burned the abbey church in 1055 and killed many of the inhabitants. Repairs were carried out between 1056 and 1058 but the building was plundered in 1079 and accidentally burned in 1100. The present structure dates from between 1189 to 1200.

The Doorty Cross, re-assembled from broken fragments, stands near the western end of the cathedral. On the western face is the image of a robed Christ above the figure of someone riding a donkey. The eastern face is of more interest, as it shows St. Peter blessing two smaller arm-linked figures; one with an Irish-type crozier is supposed to be a bishop, while the second, holding a tau or T-shaped crozier, may be an abbot. The whole, according to tradition, is a representation of St. Peter or of the church blessing Kilfenora's change from monastic to diocesan status. This would date the cross to 1152, as it seems fairly clear that it commemorates the setting up of the diocese of Kilfenora in that year.