He was appointed Prefect and "Second Person" of the royal artillery of Scotland (S. D. N. Regis Machinarii Bellitarii Prefecti) on 23 August 1569, during the Regency of the James Stewart, Earl of Moray. In 1570, Chisholm joined William Kirkcaldy of Grange in the garrison of Edinburgh Castle that remained loyal to Mary, Queen of Scots. During the following 'Lang Siege' of the Castle and Marian civil war, Chisholm travelled abroad seeking support and supplies. In February 1571 he was in London and wrote about ongoing peace negotiations, hoping that Elizabeth I of England would act to restore Mary to the Scottish throne. He hoped that the frustrating talks would be concluded soon; "I hoip seurlie within sax ouilkis (six weeks), we salbe at our wittis end and sooner."