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He was second in command of John Pickering's Regiment of Foot, one of the original twelve foot regiments of the New Model Army. When John Pickering died on 24 November 1645 he took command of the regiment; and, as was the custom then, the Regiment became known as John Hewson Regiment of Foot.
In 1647 Parliament passed an act against religious festivals, regarding them as "vain and superstitious observances" when the Mayor of Canterbury tried to enforce this act and stop Christmas there was a riot and John Hewson Regiment of Foot were sent to restore order which they did quickly. In 1648 Hewson played a key role in Pride's Purge and the Army's occupation of London.
In January 1649 he signed the death warrant for Charles I marking him as a regicide. Later that year his regiment refused to fight in Ireland until the Leveller reform programme was implemented; as a result 300 men were cashiered out of the army without arrears of pay. While in Ireland he was involved in the Siege of Drogheda and commanded an English force during the siege and battle of Tecroghan. He lost an eye at the siege of Kilkenny and was made Governor of Dublin.
He represented Ireland in the Nominated Assembly (or Barebones Parliament) of 1653 and Dublin in the First Protectorate Parliament of 1654. He then returned to England to represent Guildford in the Second Protectorate Parliament before being summoned in 1658 to the Other House (an Upper House equivalent to the House of Lords) as Lord Hewson.
On the restoration of the monarchy he fled to Amsterdam where he died in 1662.
Richard Neville (later Lord Braybrooke) in a footnote from his 1825 edition of Samuel Pepys' diary:
John Hewson, who, from a low origin, became a colonel in the Parliament army, and sat in judgment on the King: he escaped hanging by flight, and died in 1662, at Amsterdam. A curious notice of Hewson occurs in Rugge’s "Diurnal," December 5th, 1659, which states that "he was a cobbler by trade, but a very stout man, and a very good commander; but in regard of his former employment, they [the city apprentices] threw at him old shoes, and slippers, and turniptops, and brick-bats, stones, and tiles. … At this time [January, 1659-60] there came forth, almost every day, jeering books: one was called 'Colonel Hewson's Confession; or, a Parley with Pluto,' about his going into London, and taking down the gates of Temple-Bar." He had but one eye, which did not escape the notice of his enemies.
- Project Gutenberg's Diary of Samuel Pepys, January 1659-60.See January 25th. Transcribed from the shorthand manuscript in the Pepsysian Library, Magdalene College Cambridge by the Rev. Mynors Bright M.A. late fellow and president of the college (Unabridged), With Lord Braybrooke's notes edited with additions by Henry B. Wheatley.