During the 1648 Second English Civil War, he served as Parliamentarian commander in the strongly Royalist West Country and successfully suppressed a number of local revolts. Troops from his regiment took part in Pride's Purge in December which excluded moderate MPs from Parliament, while he was one of the 59 judges who signed the death warrant for the Execution of Charles I in January 1649. He was the only Irish Protestant to do so; many others, including Inchiquin, strongly opposed it and fought for the Royalists during the 1650 to 1652 Cromwellian conquest of Ireland.