The Abbey, which is located at the centre of the island, was founded in the 12th century during the episcopate of Gregoir, Bishop of Dunkeld.

Later tradition placed it even earlier, in the reign of King Alexander I of Scotland (1107–24), who had taken shelter on Incholm when his ship was forced ashore during a storm in 1123.

A Latin inscription carved above the Abbey's entrance reads: Stet domus haec donec fluctus formica marinos ebibat, et totum testudo perambulet orbemTranslated, it has been rendered thus:[2] "Still may these turrets lift their heads on high, Nor e’er as crumbling ruins strew the ground, Until an ant shall drink the ocean dry, And a slow tortoise travel the world round.

The ruins are cared for by Historic Environment Scotland, which also maintains a visitor centre near the landing pier (entrance charge; ferry from South Queensferry).

While these may derive from a variety of other monastic foundations with Columban associations, such as Oronsay Priory or Iona, Inchcolm is considered the most likely source of the manuscript's compilation, if not composition.