On the night of 9 March 1566, Jean Stewart, her mother Elizabeth, and her half-sister Queen Mary, witnessed the murder of Queen Mary's secretary, David Rizzio, at Holyrood Palace. After the "lang siege" of Edinburgh Castle in 1573, Lady Jean and her aunt Margaret Beaton were taken prisoner. She requested not be delivered to her husband, the Earl of Argyll. The English ambassador Henry Killigrew reported she was living comfortably at Regent Morton's board in June 1574, probably at Dalkeith Palace.