Nicholas Bernard, Dean of Elphin and Ardagh, acted as his spiritual counselor and wrote an account of Atherton's final days.

This was attributable to Atherton's status as an astute lawyer, who sought to recover lost land for the relatively weak Protestant Church of Ireland during the 1630s.

[10] Posthumous accusations of sexual wrongdoing also include allegations of "incest" with his sister-in-law, and infanticide of the resultant child, as well as zoophilia with cattle.

However, these allegations began to be circulated several months after his death in an anonymous pamphlet,[5] and may have been intended to further discredit the bishop's campaign to restore the finances of the Church of Ireland.

[12] Another legend describes the house of Butler, the lawyer who allegedly led the conspiracy against Atherton, as being haunted by the ghost of the bishop.