Like the most learned men of his time he was superstitious and a firm believer in "praesagious impressions"; his Essay for the Recording of Illustrious Providences: Wherein an Account is Given of many Remarkable and very Memorable Events which have Hapned in this Last Age, Especially in New England (1684) shows that he believed only less thoroughly than his son in witchcraft, though in his Cases of Conscience Concerning Evil Spirits (1693) he considered some current proofs of witchcraft inadequate.
He had much to do with the witchcraft persecution of his day; in 1692 when the magistrates appealed to the Boston clergy for advice in regard to the witchcraft cases in Salem he drafted their reply, upon which the prosecutions were based; in 1689 he had written Memorable Providences Relating to Witchcraft and Possessions, and even his earlier diaries have many entries showing his belief in diabolical possession and his fear and hatred of it.
He attended the trials, investigated many of the cases himself, and wrote sermons on witchcraft, the Memorable Providences and The Wonders of the Invisible World (1693), which increased the excitement of the people.
He left two other works in MS. - Memoirs of Reformers and Ministers of the Church of Scotland, and Analecta: or Materials for a History of Remarkable Providences, mostly relating to Scotch Ministers and Christians.
"These issues and events," he said in 1656, "have not been forecast, but were providences in things."