During the 1580s the Abbey was ransacked by the Sheriff of Donegal William Mostian and his brother Hugh Mostian. Hugh would later go on to served as a mercenary for the O'Donnell family.
In the Nine Years' War, the Abbey was used for a meeting between the rebel leadership and envoys of the Spanish King Philip II. The Abbey was the scene of fighting during the 1601 Siege of Donegal when a force led by Red Hugh O'Donnell attempted to capture the town from Crown forces led by the Gaelic warrior Niall Garve O'Donnell. During the fighting Niall Garve's younger brother Conn O'Donnell was killed.
- Lennon, Colm. Sixteenth Century Ireland. Gill and MacMillan, 1994.
- McGurk, John. Sir Henry Docwra, 1564-1631: Derry's Second Founder. Four Courts Press, 2006.
- Rowan, Alistair. North West Ulster: The Counties of Londonderry, Donegal, Fermanagh and Tyrone. Yale University Press, 1979.