[3] He has been referred to, uncharitably, as Loftus's "pale shadow"; a more balanced view is that the two men thought alike on most issues and so worked harmoniously together.

[3][1] He was immediately called to the Privy Council of Ireland by the government of Lord Deputy John Perrot, a position he held for 20 years.

[5] In April 1605, Adam Loftus died and King James I emphatically chose Jones to be Archbishop of Dublin, commencing the following November.

He was also named prebendary of both Castleknock parish of St. Patrick's and the rectory of Trim in the Diocese of Meath: Whereas, since the death of the late Archbishop, we have given an order for the supply of that See, because of same being a place so eminent within that kingdom; we took time to advise of a meet person for it; we have since upon conference with divers of our Council, found none more fit for the present time than the Bishop of Meath, in regard of his long experience in that kingdom, both in the ecclesiastical state as Bishop, and in the civil affairs as a Chancellor, wherefore we have made choice of him, and we are further pleased that he shall hold in commendam a prebend, which now he hath in possession, which he will nominate unto you.In 1605, Jones was appointed Lord Chancellor of Ireland, a position he held for the rest of his life.

He was a key ally of Sir Arthur Chichester, the Lord Lieutenant of Ireland, in his policy of extreme severity towards Roman Catholics.

The Crown was anxious to resolve the feud, and in later years Jones and Lord Howth managed to settle their differences and work together amicably.

In old age, according to Elrington Ball, Jones suffered a notable deterioration in his character; he became fretful and querulous, and quite unable to bear the robust criticism which all Irish public figures are expected to endure.

[7] His enemies would spread malicious stories, such as a farcical claim that he was a wizard, simply to enjoy the hysterical efforts which Jones, who seems to have lacked a sense of humour, would make to refute them.

Obiit Decimo Aprilis, anno reperatæ salutis humanæ 1619.The monument was restored in 1731 at the request of the then Dean of St. Patrick's, Jonathan Swift, despite his low opinion of Jones, quoted above.