Pluscarden Priory was founded by King Alexander II in 1230, who asked the Valliscaulians, a Benedictine Order, to found a community here: part of Alexander's agenda was to demonstrate his authority over what had until recently been a disputed part of his kingdom. A sister house was founded at Beauly Priory, and another at Ardchattan in Argyll. The Priory was probably finished or nearing completion when the Edward I's English army stormed through Moray in 1303. It isn't know if Pluscarden Priory suffered damage at their hands, but it seems likely. If so, repairs would have followed fairly quickly, and from 1345, Pluscarden came under the control of the Bishop of Moray from his seat in Elgin Cathedral.

The link with the Bishop of Moray did not work in the Priory's favour. Some badly judged local politics in 1390 led to Bishop Alexander Bur falling out with Alexander Stewart, the younger son of Robert II. The Bishop caused Alexander Stewart to to be excommunicated for marital infidelity. Alexander Stewart, better known as the Wolf of Badenoch responded by descending on Moray with an armed band of Highlanders and burning down Elgin Cathedral, the towns of Elgin and Forres, and Pluscarden Priory.

Repairs followed, but by 1454 Pluscarden Priory was again in a state of disrepair and the number of monks had shrunk to around half a dozen. The Pope agreed an amalgamation with Urquhart Priory, a Benedictine Priory five miles east of Elgin. A major programme of rebuilding followed, now Benedictine, which continued well into the 1500s. At the time of the Reformation in 1560 there were around a dozen monks at Pluscarden, plus Prior Alexander Dunbar living in the nearby prior's house.

On Prior Alexander's death in 1560, Mary Queen of Scots granted Pluscarden Priory and its remaining lands to the Setons. In 1587 this religious appointment was translated into a temporal Lordship, although significantly the head of the Seton family retained the legal title of Prior, ensuring that the continuity of the title was recognised in Scots law, first to George, 7th Lord Seton, thence to his son Alexander Seton, Prior of Pluscarden and later Lord Urquhart and Fyvie, Chancellor of Scotland and 1st Earl of Dunfermline.