There are several referrals in the annals of Irish History to the abbey of Tobar Patraic. The annals of the Four Masters tell of the burning of part of the Abbey in 1265. It would seem as if this burning was confined to the nave. This part of the church was rebuilt in 1270 and even today differeences in the style of the building may be notice.

In 1536 legislation was passed in Dublin dissolving Monasteries. But outside the pale, such legisation was very difficult to enforce. The same applies to Elizabeth's time. However, James I in 1603 confiscated all the lands belong to the abbey and effectively ended the presence of the Canon Regulars in the Abbey. From 1603 to 1653 the Augustian Friars (a mandicant order) may have been in charge of the Abbey. Their presence ceased there with the burning of the Abbey in 1653.

The burning of the abbey in 1653 by Cromwellian soldiery marks the second attempt to destroy Ballintubber Abbey. The Cromwellian assault was only partially successfully. The monastic buildings, the dormitories, the cloisters and domestic quarters seem to have been completely destroyed. The abbey church again escaped total destruction. All of the timber roof was consumed in fire, but the internal stone-vaulted roofs of the chancel, the four side chapels and the old sacristy remained intact.

But even Cromwellian despoliation did not put an end to divine worship in the abbey. Mass continued to be said there as it has been said for almost 750 years.