In 1580, during the Second Desmond Rebellion, the castle was defended by a garrison composed of some 70 Irish, Italian and Spanish troops, led by Captain Julian, an Italian. The Siege of Carrigafoyle Castle by Elizabethan forces under Lord Justice Sir William Pelham began on Palm Sunday. After two days, it was breached by cannon fire and taken, following which the surviving defenders were all hanged. The cannon breach remains visible to this day. Towards the end of the Nine Years War, taking advantage of the distraction of the English, Chieftain John O'Connor briefly re-occupied the castle only to be put out again in 1603 by George Carew, the Governor of Munster.