Nine years later the men of the Decies took the fortress by surprise and killed Robert Barry, brother of Giraldus Cambrensis. In the autumn of the same year (1189) the Irish, finding they could not hold the castle, decided to destroy it, but they afterwards surrendered it upon terms. From this time it appears to have been an episcopal residence for some four hundred years.
In 1218 the Bishop of Waterford wrote to Henry III. complaining that the castle of Lismore had been taken from him by Thomas FitzAnthony and Griffin FitzGriffin. The King ordered that it should be restored to the bishop.
When Robert de Bedford was elected Bishop of Lismore the fortress was transferred to him, but not without the Bishop of Waterford declaring it belonged to his see. Bishop de Bedford appealed to Rome, and after a dispute of twelve years it was finally confirmed to the see of Lismore.
In 1271 Lord Justice Audley came on a visit to the castle, and Roger de Mortimer, after he landed at Youghal as Lord Justice, was the guest of Bishop Fleming at Lismore in 1317.
Some time before his resignation in 1589, Meler Magrath, Bishop of Lismore and Archbishop of Cashel, granted the castle to Sir Walter Raleigh at a rent of £13 6s. 8d., and three years later Sir Walter sold it to Sir Richard Boyle, afterwards the first Earl of Cork, who restored and enlarged it.
His great son, the philosopher, was born in the castle in 1626.
The stronghold was besieged three times during the civil wars of 1641. It was first attacked by five thousand Irish troops under the command of Sir Richard Beling, and was successfully defended by Lord Broghill, the Earl’s third son.
The following year an unsuccessful attempt was made to burn it by the Irish.
In 1643 it was again besieged by Lieutenant-Colonel Purcell with seven thousand foot and nine hundred horse. This time Captain Hugh Croker commanded the garrison. The Earl records in his diary that the rebels demanded the surrender of the fortress, but “we retorned them defyance.” None of the defenders were killed, but their enemies lost about three hundred in killed and wounded. The following month cannon was brought to bear on the stronghold, and a breach was effected in the brewhouse, but it was quickly repaired with earth, and the fire from the castle was so great that the enemy did not dare to storm the opening. The guns were then shifted to the south-west, and the orchard was attacked, but the shots from the turrets protected the curtain wall.
After a siege of eight days, the Earl’s sons, Lords Dungarvan and Broghill, landed at Youghal and made a treaty with Lord Muskerry for a six days’ truce. Of the besiegers twenty were killed, while the defenders escaped injury.