Another James Butler (1665-1745) succeeded his grandfather as second duke of Ormonde in 1688, the same year that a constitutional crisis erupted in England
when William of Orange landed in Devon. In the ensuing war Ormonde fought on William's side. In 1689, Kilkenny Castle was taken over by the Jacobite
Viscount Galmoy who lodged barrels of powder and shot in the cellar of the 'Round Tower'. The victorious King William was a guest of Ormonde's at Kilkenny Castle before his return to England.
Some alterations were made to the interiors of the Castle to suit the needs of the second ducal couple and a new building was begun on the eastern side of the courtyard. Mary Somerset, (1665-1733) 2nd duchess of Ormonde, visited Kilkenny and wrote enthusiastically about her reception there. 'I have been received with as much respect as the greatest woman in the world could have been both by Civil, Military and Ecclesiastical persons'. But, following Ormonde's involvement in a Jacobite plot of 1715, a bill of attainder for treason was passed against him.
In 1717 an inventory was taken of the contents of the castle for appraisal on behalf of the Commissioners of Forfeited Estates. A sale of the goods of the castle was advertised in the Dublin Gazette of 1718, but the extent of this has not been established. By the time inventory was taken for the sale, the interior of the castle was suffering from neglect. The damask hangings of the state bed, which had gold and silver fringing were described as being 'much tarnished'. Decay was widespread and even the curtains on the ducal bed had been 'cut and carried away by thieves'. Ormonde's brother, Charles, Earl of Arran, was permitted by an act of the English Parliament to purchase some of the Irish properties including Kilkenny Castle in 1721 and thus secured ownership of the castle for the family.