Reorganized from 1967 to 1970 by Louis Miquel, a pupil of Le Corbusier, the museum is again the subject of a total renovation and an enlargement from October 2015.

Three years later, the completely renovated museum was inaugurated on November 16, 2018 in the presence of the President of the Republic Emmanuel Macron, the Minister of Culture Franck Riester and the Mayor Jean-Louis Fousseret.

The collections of the musée des Beaux-Arts et d'Archéologie de Besançon are divided in three categories: archaeology, painting, and drawing cabinet.

In 1819 Pierre-Adrien Pâris, the King's architect, added his collection (38 paintings and 183 drawings including those of Fragonard).

Jean Gigoux gave the museum his collection in 1894 (over 3000 drawings and 460 paintings of Spanish, English, Northern and German schools), and finally George Besson and his wife gave the museum their collection in 1960 (112 paintings and 220 modern and contemporary drawings).