[2] In 1172, King William I, the Lion, made grants to the church of the Holy Trinity of the Bishopric of Moray and Bishop Simon de Tosny.

Formal permission for the permanent move to Spynie was given by Pope Innocent III to Bishop Bricius de Douglas in April 1206 and the transfer was probably made by 1208.

This manuscript dates from the early 14th century but appears to have been compiled between 1292 and 1296 and was apparently for the use of English administrators during King Edward I of England's occupation of Scotland.

In this period Alexander Stewart, Earl of Buchan, otherwise known as the Wolf of Badenoch, attacked and burned Elgin Cathedral in June 1390.

[12] It is thought that Bishop John de Winchester (1435–60) was responsible for moving the main gate to the east wall which contained a strong portcullis.

[13] The architectural detail of the upper section of the gate remains and shows the gatekeeper's room complete with a small fireplace.

John, as well as being the Bishop of Moray, was also the king's Master of Works and had been responsible for alterations to the castles at Inverness and Urquhart as well as the palace at Linlithgow.

English prisoners were held at Spynie during the war known as the Rough Wooing, including Edward Sutton, 4th Baron Dudley who was taken at Hume Castle in December 1548.

[23] Christopher Rokeby, an agent provocateur of Elizabeth I of England, who had tried to lead Mary, Queen of Scots, into a plot with English Roman Catholics, was imprisoned in Spynie Castle in 1566 for eighteen months during Bishop Patrick Hepburn's tenure.

[24] Hepburn fell foul of the Privy Council for sheltering his relative Bothwell at Spynie in 1567 who had fled from the battle of Carberry Hill first to Huntly Castle.

As part of the pacification following the abdication of Queen Mary, Regent Morton, in a meeting of the Privy Council at Perth on 23 February 1573, ordered that the castle be made available to the Crown, if needed:the hous of Spyne salbe randerit and deliverit to oure Soverane Lord and his Regent foirsaid quhen it salbe requirite on XV dayis warning, without prejudice of ony partiis rycht.

[27]On 29 July 1587, King James VI gave the castle and estate to Alexander Lindsay, 1st Lord Spynie; and they remained in his hands until he surrendered them back to the Crown in December 1605.

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.

[32] 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.

Local people plundered the walls for stonework for building works until the early 19th century when it passed into the ownership of James Dunbar-Brander of Pitgaveny.