In this period, Scougal showed himself to be an extremely religious ideologue, preaching against papists and playing a leading role in the national witchhunt of the 1660s.

Perhaps because of his known and well-established religious fervour, hostility to Scougal's newly shown pro-episcopacy sentiments was comparatively muted.

Scougal took an active role in the suppression of Quakerism and was part of a prosecution of James Gordon, the parson of Banchory-Devenick, who had written the Catholic-leaning theological tract called The Reformed Bishop (1679).

His second wife was Anna, daughter of William Congalton of that Ilk, widow of Robert Lauder of Gunsgreen (near Eyemouth, Berwickshire).

[4] By his second wife, Jean Wemyss (possibly Margaret's sister), he had a daughter Katherine who married Bishop William Scrogie.