The De Institutione Musica, one of the first scientific treatises of Boethius, exposes the relationship between man and music based on the musical harmony of body and soul, where Plato and Aristotle appear to confirm and support Pythagoras, who would be the creator of this anthropology. In our analysis, the teaching of Boethius comes from the neoPythagorism of Nicomachus of Gerasa, and it is incompatible not only with the corresponding doctrines of Plato and Aristotle, whom Boethius says to be honoring with the translation of their works, but with other treatises, especially the Contra Eutychen, which is analyzed here, since it has a strong anthropological component. The question we ask is whether Boethius was aware of this doctrinal incoherence in his work. Our answer is positive, that is to say, that although the anthropologies are not compatible, Boethius' mind is not in contradiction with itself, because the Contra Eutychen and in general the theological treatises are the author's original answers to theological problems, while De Institutione musica and in general the scientific treatises are not original nor pretend to be, but depend on their sources.