The collections of the Musée comtois owe much to one man: Abbé Jean Garneret. Inspired by the Scandinavian model, he embarked on fieldwork in ethnology in order to preserve a world that was disappearing under the effect of the major economic and social changes of the century. Starting in the 1930s, he collected objects that bore witness to life in the Franche-Comté region, first on his own initiative and then at the request of the Direction des Musées de France and the Musée National des Arts et Traditions Populaires.
Founded in 1946 and housed in the Citadel since 1960, the Musée comtois has expanded its collections thanks to numerous donations from private individuals. Not to mention the Folklore comtois association and its key role: in 2007, for example, it donated a very important collection of negatives to the City of Besançon.
Some of the collections have been partially digitized and are available online on the City of Besançon's Mémoire vive website and on the Puppetry Arts Portal.
