He was the author of two learned works, Critical Essay on the Ancient Inhabitants of the Northern Parts of Britain (1729), and Civil and Ecclesiastical History of Scotland, 80 to 818 (published 1853).
[1] On 26 May 1684 he received the clerical tonsure; on 10 March 1691 was promoted to the priesthood, and afterwards spent a few months at Notre Dame des Vertus, a seminary of the Oratorians near Paris.
In 1720 his brother Lewis, in what may be a formal letter to the vicar-general of the Bishop of Apt, contradicted a report that Thomas had concurred in an appeal to a general council against the condemnation of Pasquier Quesnel's 'Moral Reflections' by Pope Clement XI.
[1] The results of Innes's researches in Scottish history and antiquities were communicated to scholars who sought his assistance.
Francis Atterbury and Thomas Ruddiman were among them, and Robert Keith was given materials for his Catalogue of Scottish Bishops.
Harry Maule of Kelly, author of the 'Registrum de Panmure,' are printed in the appendix to John Stuart's edition of that work, 2 vols.