Jones thus became caught up in the scandal surrounding the notorious body-snatchers Burke and Hare, but was cleared by the investigating committee.

Jones contributed the anatomical drawings of sections of the eye that appeared in Mackenzie's classic treatise.

[5] Jones travelled to Cork in 1835, and for a time he engaged in medical practice there, devoting himself chiefly to diseases of the eye and ear.

In 1872, on behalf of the Camden Society, Jones edited an account of the life and death of Bishop Bedell of Kilmore, who was an ancestral kinsman who died in the Irish Rebellion of 1641.

Jones disagreed with the Darwinian theory of evolution, regarding it as a "mere conceit unsanctioned by science," and published a book in 1876 propounding this view.