In 1606, King James restored to the bishopric of Moray the endowments that remained. Bishop John Guthrie, who was a well known royalist, ceased to be the bishop in 1638 when all bishops were deposed by the general assembly – he and his family continued to live at Spynie however. Guthrie refused to subscribe to the Covenant and prepared the castle for a siege which duly arrived in 1640 in the form of Covenanter Col. Sir Robert Monro and his 800 men. surrendered the castle immediately on 16 July and the castle was disarmed, however he was allowed, together with his wife and servants, to stay within the castle. Although under house arrest, Guthrie was forced to pay for the upkeep of the garrison of twenty four men. In September 1640, Guthrie was imprisoned in Aberdeen on rather dubious accusations. The castle was then granted to the Earl of Moray by King Charles I. Elgin and surrounding areas were staunchly anti-Royalist and after his victory against the Covenanters at Auldearn on 9 May 1645, James Graham, Marquis of Montrose turned his attention towards Elgin. The Laird of Innes and Grant of Ballindalloch and some burgesses from Elgin prepared the castle for a siege. Montrose occupied Elgin and burned the homes of leading Covenanter supporters in the town and the farmyard buildings belonging to Spynie but did not attempt to take the castle. Spynie had become the centre for the Covenanters in the area and this fact had not gone un-noticed with the Royalists. The Marquis of Huntly laid siege to the castle in late 1645 leaving Lord Lewis Gordon in charge but the castle's defences held until it was relieved by John Middleton, the future Earl of Middleton.