Following the abbey's seizure by the Crown, the buildings and land were leased to Thomas Clinton, one of Queen Elizabeth I's officers in County Kerry. On 12 December 1588, the Crown transferred the abbey and its estate to Captain Thomas Spring of Castlemaine, a Protestant nobleman who had served with distinction during the Desmond Rebellions and was a grandson of Thomas Spring of Lavenham. The grant included a special clause to rebuild the domestic buildings of the abbey in a castle-like manner, so that the building could serve as a defensive structure. Captain Thomas Spring's son, Walter Spring, was High Sheriff of Kerry in 1609. His grandson, Walter Spring, was raised as a Roman Catholic and fought in the Irish Rebellion of 1641. As a result, the abbey was attacked by a Cromwellian army during the Irish Confederate Wars. The fortified domestic buildings were demolished by cannon fire, while the church was partially damaged. Following the suppression of the rebellion, almost all of Walter Spring's lands were seized by Oliver Cromwell and he was subsequently dubbed 'The Unfortunate'. Killagha Abbey was granted to a Cromwellian soldier, Major John Godfrey. Despite the readjustment of lands in Ireland under Charles II, the grant to Major Godfrey was confirmed in the Act of Settlement 1662. However, with the abbey's manor house destroyed, the abbey was no longer used as a dwelling place. The Godfrey family built a new stately home in Milltown in 1772, which they named Kilcolman Abbey, but was also known as Bushfield House. It was abandoned and demolished in 1977.