Inchmahome there was a church on the island before the priory was established. The priory has a long history of receiving many notable guests. King Robert the Bruce visited three times, in 1306, 1308 and 1310. His visits were likely politically motivated, as the first abbot had sworn allegiance to Edward I, the English King. In 1358 the future King Robert II also stayed at the priory. In 1547 the priory served as a refuge for Mary, Queen of Scots, aged four, hidden here for a few weeks following the disastrous defeat of the Scots army at the Battle of Pinkie
Wars of Scottish Independence around 2,000 Scots had been slain. Edward Balliol then had himself crowned King of Scots, first at Perth, and then again in September at Scone Abbey. Balliol's success surprised Edward III, and fearing that Balliol's invasion would eventually fail leading to a Scots invasion of England, he moved north with his army. In October, Sir Archibald Douglas, now Guardian of Scotland, made a truce with Balliol, supposedly to let the Scottish Parliament assemble and decide who their true king was. Emboldened by the truce, Balliol dismissed most of his English troops and moved to Annan, on the north shore of