According to historian James Anthony Froude, William made the abbey "a nest of sodomy and fornication – the very aisles of the church itself being defiled with the abominable orgies of incestuous monks and nuns". This is based on an account by Cardinal John Morton who investigated on behalf of Pope Innocent VIII after obtaining a papal bull, though it is not clear if a formal visitation took place. The charge was seen as incredible by another historian, F. A. Gasquet, who noted that an obituary said "Nobody showed more care in the worship of God than our reverend father, abbot William Wallingford, or more kindness in works of piety. Nobody showed more devotion to the fervour of faith, hope and charity. None of the ancients before him had shown so much generosity in putting up buildings to the praise and glory of this monastery."
