In March 1653, the Rump issued a full pardon for his time as a Royalist, opening the way for his return to public office. Following the dissolution of the Rump in April 1653, Oliver Cromwell and the Army Council nominated Cooper to serve in Barebone's Parliament as member for Wiltshire .  On 14 July, Cromwell appointed Cooper to the English Council of State , where he was a member of the Committee for the Business of the Law, which was intended to continue the reform work of the Hale Commission.  Cooper aligned himself with the moderates in Barebone's Parliament, voting against the abolition of tithes .  He was one of the members who voted to dissolve Barebone's Parliament on 12 December 1653 rather than acquiesce to the abolition of tithes.