[4] He was briefly minister of North Leith Parish Church, being appointed in 1638, but was deposed for his refusal to sign the Covenant.
[5] A strong supporter of episcopacy, he fled to England in 1639, and in Scotland, he was officially deposed for abandoning his duties and "immorality".
He played a key part in the defence of Newcastle upon Tyne in October 1644 during the Siege of Newcastle during the English civil war, when the town held out for seven months against the Parliamentary forces, and he was one of the "diehards" who took refuge in the Castle when the town fell.
Whilst most of the garrison were allowed to depart, Wishart was imprisoned in the "Thieves Hole" at Edinburgh Tolbooth for his exploits with the James Graham, Marquess of Montrose, whose devoted champion and personal friend he was, and of whom he wrote a laudatory biography, published in the Netherlands in 1647.
The book was so hostile to Montrose's opponents that the Royalists made half-hearted efforts to suppress it as being too inflammatory.