It would seem that the History of the County of Brecknock was conceived c. 1800. The first volume appeared in 1805, the second (dedicated to Edward Davies) in 1809. In his later years Jones was very friendly with Thomas Price (Carnhuanawc, q.v.). He d. 15 Jan. 1812, and was buried at Llangamarch. He was Welsh-speaking, author of an unpublished English version of Ellis Wynne's Bardd Cwsc, and at one time owner of the ‘Book of Aneirin’ — this was given him by Anthony Bacon (q.v.) and passed after his death into Thomas Price's hands. He had intended writing a history of Radnorshire, and contributed several papers to the Cambrian Register and to Archaeologia. In 1905, Edwin Davies (q.v.) published a volume, Theophilus Jones, Historian, containing these papers, Jones's letters to Edward Davies and Walter Davies (Gwallter Mechain, q.v.), and a biography by Gwenllian E. F. Morgan (q.v.).

To this day, Jones's work is the best of our Welsh county histories — a work of diligent and careful research. The author's prejudices are too obvious to cause trouble — his anti-Popery, his dislike of Dissent and of Methodism (yet his article on Howel Harris, reprinted in the memorial volume mentioned, is not altogether unkindly), his prosaic nature which blinded him to the merits of Henry Vaughan the poet. A second edition with some additions was published by Edwin Davies in 1898 in one volume. In 1909-11 Davies began bringing out a third edition, which was completed by the county historical society in 1930, with copious additions from the collections of the first baron Glanusk (see under Bailey of Glanusk). In this handsome four-volume edition the work is indispensable for the student of the history of Brecknock and of Brecon.