Scotus College can trace its ancestry back to 1714 and the establishment of a secluded seminary on a small island in Loch Morar. This seminary was forced to close and the fleeing students found refuge at Scalan in Glenlivet. Scalan persevered through troubled times and eventually, after eighty years service, handed over its mantle to Aquhorties and then to Blairs College until its closure in 1986.

Senior seminaries were a much later creation, and initially the seminary planned for Glasgow had to be mothballed due the influx of Irish Catholics and their immediate needs. However, in 1874 Archbishop Eyre opened St Peter's College, Partickhill, which in 1892 moved to New Kilpatrick, Bearsden. Unfortunately, disaster struck in a fire of 1946 and the College was moved to Darleith to become St Peter's College, Cardross. Much later St. Peter's College was relocated at Newlands in Glasgow where it lived out its final four years.

On the east coast Archbishop Gray opened Drygrange College near Melrose in 1953, This seminary later moved to Gillis in Edinburgh.

On November 1, 1984 an interdiocesan seminary was opened on the current site of Scotus. The newly formed Chesters College was to be, along with Gillis College, the forerunner of Scotus. Scotus was officially opened on October 4 1993 and can be viewed as the coming together of East and West, resulting in the first ever national seminary in Scotland.

The new chapel was built and opened in 1997.