The library was founded in 1694, when the Benedictine Abbot Jean-Baptiste Boisot (1638–1694) bequeathed his personal collections to the Abbey Saint Vincent in Besançon, under the sole condition that it would be publicly available.

[2] A large part of the collection came from Nicolas Perrenot de Granvelle and his son Antoine.

During the French revolution confiscations were made from the religious communities and from emigrants living in the region.

The 14th-century manuscript "The Day of Judgement", catalogued as Ms. 579, contains 89 miniatures depicting the action of the play and three neumed musical pieces.

[4] Besançon BM 434 contains textbooks for Charles V: book of educations of the princes, 49 miniatures, made by several artists having worked on the copy of Travels of Jean de Mandeville.