George, Lord Seton garrisoned the castle in support of Queen Mary in 1572 during the civil war in Scotland. According to two chronicles, the "Diurnal of Occurents" and the "Historie of James the Sext", Niddry was attacked twice, in April and June. In April, Captain Scougall with forewarning repelled a night attack. He suspended heavy timber beams around the tower and released them on a party climbing scaling ladders. The garrison of Edinburgh Castle supported Niddry by attacking Merchiston Castle, which was held for James VI, as a diversion.