On 11 September 1322 he was very quickly pardoned for his part in the rebellion having returned to the King's side, raising another 500 men for him in 1325. John Charlton's authority on the Welsh border was threatened by The Earl of Arundel who became Justice of Wales in 1322, and Warden of the Welsh Marches in 1325, establishing his base as Constable of Montgomery Castle. In the autumn of 1326, Charlton's former ally Roger Mortimer (whose daughter Maud was married to Charlton's son John), and Queen Isabella took action against the Despenser family and other unpopular advisers to King Edward. Arundel remained loyal to the king, which gave Charlton the opportunity to rid himself of his rival by arresting and executing him (at Shrewsbury  or, possibly, Hereford) under the orders of the Queen. Thomas Charlton, Bishop of Hereford who was Lord Privy Seal from 1316-1320 was John's brother. On 29 June 1337, after King Edward III had taken power from Queen Isabella, John Charlton was appointed Chief Justiciar of Ireland and his brother Thomas became Lord Chancellor of Ireland. Within a year John had returned to England, following a dispute. John Charlton split his last years between his properties at Apley Castle in Shropshire, Charlton Hall in Shrewsbury (the site now occupied by the theatre) and Powis Castle in Mid-Wales. In his later life he was a patron of Strata Marcella abbey, and was buried at the Franciscan Greyfriars Abbey in Shrewsbury, next to his wife, her father and grandfather. A fourteenth-century stained glass Jesse window, now in St Mary's church, Shrewsbury, but originally in the Greyfriars, shows at the bottom right hand corner, a knight bearing the arms of Powys who is probably Charlton. He was succeeded by his son John Charleton, 2nd Baron Cherleton. A daughter, Isbella, married John Sutton II. Their descendant Edmund Sutton would marry Joyce Tiptoft, daughter of Joyce de Cherleton, co-heiress of Edward Charleton, 5th Baron Cherleton, last to hold the title Baron Cherleton.