The collections comprise three sections: archeology, ancient art and contemporary art.

Archeology: It is a matter of the archeological discoveries in the area of Jura, from the Neolithic to the Merovingian era.

Ancient art:

• Burgundian and of Franche-Comté sculptures from the Middle Age to the 18th century (G. Lullier, F.-M. Rosset, C.-F. Attiret),
• French paintings 17th century and 18th century (S. Vouet, E. Allegrain, Ch.-A. Coypel), Italian Old Master Giambattista Pittoni, Italian ones (F. Albani, L. Giordano, G. Assereto) and Nordic ones (Maître de Saint-Gilles, P. van Boucle, C. Gysbrechts).
• Paintings from the 19th century (J. B. Jongkind, G. Courbet), in particular from local artistes (J.-D. Attiret, A. Pointelin, J. Machard, G. Brun).
• The History of Franche-Comté is represented by conquest scenes painted by van der Meulen, Martin des Batailles and Martin des Gobelins.

Contemporary art:

• Paintings of artists who worked in France since the 60’ having for theme art and corporation: the Narrative Figuration (Fromanger, Rancillac, Monory, Erró) and the New Realism (Arman, Villeglé, Deschamps).
• Temporary expositions:
  • 1985: Claude-Max Lochu, Erró
  • 1987: Yayoi Kusama
  • 1991: Charlemagne Palestine
  • 1994: Peter Stampfli
  • 1997: Yan Pei-Ming
  • 1999: Jacques Monory
  • 2000: Peter Saul
  • 2003: Bernard Rancillac
  • 2004: Gérard Deschamps
  • 2005: Gérard Fromanger
  • 2006: Helen Frik: The Frik Collection
  • 2006: La Figuration Narrative
  • 2007: La sculpture du XVe siècle en Franche-Comté
  • 2008: Swetlana Heger
  • 2009: Jean-Olivier Hucleux
  • 2010: Erró. 50 ans de collages
  • 2011: Ida Tursic et Wilfried Mille
  • 2012: Laurent Pécheux
  • 2013: Philippe Cognée
  • 2013: Gérard Schlosser

• Musée des Beaux-Arts de Dole
• Musée des Beaux-Arts de Dole sur le site des Musées de Franche-Comté