The college, originally called Collège des Aicelins, was founded in 1314 by Gilles I Aycelin de Montaigu, Archbishop of Narbonne and Archbishop of Rouen. It changed its name after it had been restored in 1388 by his relative Pierre Aycelin de Montaigut, Bishop of Nevers and Laon.
In 1483 Jan Standonck became Master of the College and made it prosper. Under his leadership and that of his disciple Noël Béda, Montaigu was one of the leading theological colleges of Paris. Students at the college included Erasmus of Rotterdam, John Calvin, and Ignatius of Loyola (before moving to Collège de Sainte-Barbe). Other notable students were the influential Portuguese teacher and diplomat Diogo de Gouveia. At least four Scots also attended: philosopher John Mair (who went on to teach theology there), historian Hector Boece, royal advocate Patrick Paniter and Reformer John Knox. Another Scot, George Dundas, may have also attended.
In 1792, some of the buildings were converted into a hospital and a military prison. The prison was closed in 1836, and pulled down in 1842. In 1844-1850, the Sainte-Geneviève Library was constructed on the site.
- E F Robertson, J J O'Connor. "John Maior". School of Mathematics and Statistics - University of St Andrews, Scotland. Archived from the original on 25 August 2011. Retrieved 3 December 2011.
- Erasmus, Desiderius (1997). Colloquies: Collected Works of Erasmus 39-40. University of Toronto Press. p. 755. ISBN 0-8020-5819-1.
- Tronel, Jacky (14 March 2010). "Montaigu, ancien collège transformé en pénitencier militaire". prisons-cherche-midi-mauzac.com (in French). Retrieved 22 August 2017.