In 1584, when he was upwards of eighty years of age, he was concerned with the so-called “treasonable proceedings of the Earls of Angus and Mar, the Master of Glammis, with their colleagues and accomplices, and for reception, support, intercommuning, and defence of the said persons and their associates in the said treasonable act committed in the month of April last bypast".
John Duncanson must have been very active, because he was, along with others, excluded from the remission, pardon, and protection granted by the King to the “bailies, councillors, community, and inhabitants, with their wives and children".
He was subsequently presented to the Vicarage of the Chapel Royal on 17 March 1567 then later demitted the post before 25 January 1574, on appointment to the Sub-Deanery.
He was elected Moderator of the General Assembly on 7 August 1574, also Commissioner of Galloway, and was appointed with others to draw up the Second Book of Discipline in 1576 and 1578.
[1] He wrote a Reply to Tyrie, the Jesuit's Refutation of Knox's Answer to a former work, which was appointed to be revised by the General Assembly in March 1673.