In 1625 he succeeded his father as dean of Ardagh until he was appointed Dean of Kilmore in 1637. In 1638 he was also collated Archdeacon of Kilmore.
During the Irish Rebellion of 1641 he was forced to surrender his castle at Belananagh, County Cavan to the O'Reillys. Whilst in captivity he offered to go to Dublin to present a petition of behalf of the rebels, where he was able to report on their plans. In December 1641 he was able to escape with his family to Dublin. He then did much to mitigate the sufferings of the Protestants during the war, including making a trip to London to collect money for their relief. He served as the head of a "Commission for the Dispoiled Subject" which documented losses of Loyalists at the hands of the Irish rebels; Jones presented a report to the British House of Commons in March 1642, and in 1652 published An Abstract of some few of those barbarous, cruell massacres and murthers of the Protestants and English in some parts of Ireland, drawn from the commission's depositions.
On 27 October 1645 he was raised to the episcopy as the bishop of Clogher on the recommendation of the Marquis of Ormonde and was consecrated in Christ Church, Dublin, on 9 November. He was allowed to retain the archdeaconry of Killaloe and other preferments in commendam. In the following year he was appointed vice-chancellor of Trinity College, Dublin, to which he presented the 'Book of Durrow' and the Book of Kells, and in 1651 the exotically designed oak staircases which led to the gallery of the new library. On 25 May 1661 he was translated to the bishopric of Meath. The sermon he gave at the consecration of his brother Ambrose as Bishop of Kildare in June 1667 was published.