During the English Civil War, William sided with the parliamentarians. The town of Grantham was captured by Royalists on 23 March 1643 and on 11 April he was indicted for high treason. On 11 May 1643, however the town was recaptured by Oliver Cromwell and Clarke was released. Following the war William attained wealth and landholdings, but lost much of his fortune following the restoration.
