Following the end of the war, Jones was selected as one of the judges of King Charles I, and attended the trial with great regularity. Jones was the forty-second signatory of the fifty-seven commissioners that signed the death warrant that effectively authorised the execution of the King. After execution, Jones was elected a member of the first two Councils of State of the Commonwealth of England In July 1650, Jones was voted one of the commissioners to assist the lord deputy in the government of Ireland, and was reappointed for two years longer on 24 August 1652. His colleague, Edmund Ludlow, described him as "discharging his trust with great diligence, ability, and integrity, in providing for the happiness of that country, and bringing to justice those who had been concerned in the murders of English Protestants".