One of his best-known works is Myth, Magic, and Morals from 1909, later reissued under the title The Origins of Christianity. This has been read both as a strong criticism of the Jesus myth theory, making Conybeare a supporter of the historical Jesus; but also as an attack on aspects of orthodox Christianity itself. He returned later in 1914 to make a direct assault on leading proponents of the time of the Jesus-myth theory.
Coneybeare also worked as a translator and translated two volumes of Philostratus' The Life of Apollonius of Tyana for the Loeb Classical Library. He also translated The Testament of Solomon.
Rituale Armenorum Being the Administration of the Sacraments & the Breviary Rites of the Armenian Church Together with the Greek Rites of Baptism & Epiphany edited from the oldest manuscripts (1905) with Arthur John Maclean
Selections from the Septuagint According to the Text of Swete (1905) with St. George Stock, later as A Grammar of Septuagint Greek online
The Armenian version of Revelation, Apocalypse of John the Divine (1907) editor
The Ring of Pope Xystus, Together with the Prologue of Rufinus (1910)
The Life of Apollonius of Tyana: The Epistles of Apollonius and the Treatise of Eusebius. Philostratus (1912) translator, Loeb Classical Library, two volumes
A Catalogue of the Armenian Manuscripts in the British Museum (1913)