Back at Westminster he attended regularly the ‘court of justice’ which tried Charles I (whom he held responsible for the Irish massacres of 1641), signed the death warrant, and was appointed (13 Feb. 1649) one of the council of six set up by the Rump, and an alderman of Denbigh (Sept.). He celebrated the occasion by having an elaborate pedigree emblazoned by his kinsman Robert Vaughan of Hengwrt. He was assiduous at the council table and a zealous member of the Commission for the Propagation of the Gospel in Wales (22 Feb. 1650) till appointed (2 July 1650) to accompany Ludlow to Ireland as first of three commissioners responsible for its civil government; his Welsh duties had to be fitted in with his periodic crossings to and fro from Ireland, where his chief work lay from 1651-4. In 1655 he was made a commissioner for North Wales under Berry in the régime of Major Generals. His first wife, a devout disciple of Morgan Llwyd (q.v.), had d. in Ireland (19 Nov. 1651), having borne eight children, of whom only one survived; and early in 1656 he m. Katherine Whetstone (b. 1606), sister of Oliver Cromwell and widow of a Roundhead officer (who had previously taken her with him on a Dutch campaign), but herself dubbed Royalist because she recoiled from the king's execution. (Notes and Queries, VII, ix, £303.) He settled £300 a year on her, and Oliver added an annuity of £150. The Protector put his brother-in-law on his new Council of State (June), and in Aug. Jones was elected to represent both Denbighshire and Merioneth (choosing the latter constituency) in the 2nd Protectorate parliament, where he was an active debater, especially in the discussions leading to the Humble Petition and Advice. Next year he was removed to Cromwell's ‘Other House’ with the title (rarely used) of ‘lord Jones’, and shortly before Cromwell's death he was again made a commissioner for Ireland.

When the Protectorate petered out with the resignation of Richard Cromwell, Jones was a leading spirit in the restored rule of the Rump, serving on the Committee of Safety of seven (7 May 1659) and its successor the Council of State of twenty-one (14 May). He was used mainly in Ireland, though he had to combine his duties there with the governorship of Anglesey (July), where he tried to stem the reaction by keeping his old Puritan and Republican associates in power. On 18 Aug., Ludlow left him in charge of the army in Ireland, but he was hampered in resisting the schemes of Monck (the drift of which he early realized) by storms which delayed news from England and by lack of authority with the officers, and on 19 Jan. 1660, Monck's adherents there had him arrested and impeached in London with the other Irish commissioners. Released on parole with a pass to Chester (5 May), he visited his son, for whom he vested his property in eleven trustees, and put his papers into safe keeping before returning to London to be arrested in the street (2 June) and — his name having been excluded from the Indemnity Act of 20 Aug. — tried as a regicide. He comported himself with great dignity, and was executed on 17 Oct. 1660.

Archbishop John Williams (q.v.) called him in 1647 ‘the most universally hated man’ in North Wales, but the impression is not confirmed by correspondence about his candidature for the 1656 parliament (Cal. Wynn Papers, 1834, 2108, 2116, 2118-9, 2122-3). Henry Cromwell, who distrusted his republicanism, and probably influenced Richard to stop his wife's annuity in March 1660, accused him of having ‘acted very corruptly’ in Ireland, but the charge lacks corroboration. His speculations in land with the debentures issued on his arrears of pay — including an interest in the crown lordship of Bromfield and Yale (with which he tried to tempt Henry Cromwell), in the ecclesiastical manor of Gogarth (which he offered to re-sell to the Mostyns), in the manors of Llandegla, Gwytherin, and Meliden (bought by a syndicate for £3,797 in 1650) and Uwchterfyn (c. 1652) and an offer to buy up a mortgage on Brynkinallt (1653) — were normal and legal transactions, and it was on the ground that his absence in Ireland had placed him at a disadvantage in the land sales that parliament in 1657 voted him a further £3,000 in Irish lands to cover outstanding arrears. How much of this wealth (or, for that matter, of his nominal salary of £1,000 as Irish commissioner) ever actually came to his hand may be doubted: certainly he was often in straits for ready cash in Ireland. Berry and Ludlow both speak warmly of him, and even the biting lampoon of 1657 on Cromwell's ‘lords’ (Harleian Miscellany, iii, 470) dealt gently with Jones.

The depth of his religious convictions is evident in all his letters. He was in regular correspondence with Morgan Llwyd, Vavasor Powell (q.v.), and the other leaders of Welsh Puritanism from Ireland, where he had some of Llwyd's work printed, though he found him too ‘parabolical’ for the plain man, and Powell too fond of hair-splitting and ‘disputeing’; Jones himself shared Cromwell's dislike of dogmatism and dread of anarchy, religious or political. He shrank from the consequences of a free vote before the Commonwealth had ‘time to take root’, and defended expedients that shocked the doctrinaire republicans; his hatred of ‘feudal tyranny’ was based not on Leveller principles, but on that of security for the small freeholder. For all his city upbringing he remained a countryman at heart, with the Welsh countryman's feeling for his family, his shrewdness in bargaining, and his love of rustic imagery. Even his land-hunger was the peasant's rather than the townsman's or the social climber's; in selling he preferred a modest price from the sitting tenant to a fancy one from a speculative rack-renter; he denounced profiteering at the expense of the needy debenture-holder; and when in 1653 his own Merioneth tenants defaulted because a bad season had left their cattle unsaleable, he offered to take as rent lean cattle shipped from Holyhead for fattening in Ireland. In Ireland itself he had more hope of the peasant than of his lord; but here his whole view was distorted by legendary tales of the massacres, and his only constructive proposals were evangelization (preferably from Wales) with firm and uncorrupt government. A tireless and methodical administrator, he recognized his own qualifications as ‘too narrow for the Ministers of any Commonwealth, but Sir Th. Moore's.’

He kept in touch with all his family, promising himself to do something for his ‘poor relations’ in Ardudwy as soon as things were settled. He looked after both the spiritual and the temporal interests of his niece Lowry (1623-1694), daughter of his eldest brother EDWARD JONES (who had died after a year of marriage, and from whom he probably inherited Bryn-y-ffynnon, Wrexham), and also those of her children — one of whom became father of Ellis Wyn of Lasynys (q.v.) — when their father Ellis Wynne of Glynn (whom she m. in 1639) d. c. 1653; by her second husband, a grandson of Edmund Prys (q.v.) she had a son Edmund Price (1662-1718), entered as ‘pauper’ at Jesus College, Oxford, in 1682 (graduating 1685), who became vicar of Clynnog 1692, inherited Maes-y-garnedd, but disposed of Gerddi Bluog (the Prys estate) in 1710. Another brother, HUMPHREY JONES (d. c. 1690), mercer, of Paternoster Row, was John's banker, business agent, and executor, and his son's faithful counsellor; Humphrey's own son, THOMAS JONES, went to Oxford in 1666 and became successively vicar of Oswestry, 1680, rector of Darowen, 1684, and vicar of Llangollen, 1702. HENRY JONES, John's third brother, became deputy governor of Dublin under Sir Theophilus Jones (see under Michael Jones, d. 1649) and was still in Ireland in 1659, but d. before 1664. RICHARD JONES, the youngest brother, and his sister Lowry, stayed in Ardudwy, and to them John wrote (with some diffidence) in Welsh.