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
Scottish religion in the seventeenth century the Catholic Mary, Queen of Scots (1561–67) eventually ended in civil war, deposition, imprisonment and execution in England. Her infant son James VI was crowned King of Scots in 1567. He was brought up as a Protestant, while the country was run by a series of regents. After he asserted his personal rule from 1583 he favoured doctrinal Calvinism, but also episcopacy. James claimed his authority as monarch and head of the Church came directly from God, the so-called theory of Divine Right, and was not subject to 'interference' by Parliament or church leaders. When he also became King of