The Museum exhibits works of art taken from other churches in town and in the territory of the diocese of Florence, which can no longer be perserved in the original churches for safety reasons. The museum was openend only in 1996 after long restoration works that were necessary to rebuilt the rooms after the explosion of via dei Georgofili in 1993. The works of art had already been collected and made accessible only to scholars for over ten years in the diocesan warehouse.

The restoration plan, which was possible thanks to the contribution of the Regional Administration of Tuscany, has implied building the necessary systems and adding value, thanks to a new layout, not only to the exhibited works, but also to the church, dedicated to Santo Stefano and Santa Cecilia. This building already existed in 1116, although its Romanesque facade had been built in different stages starting from the lower section (1233). The interior of the church, restructured in the 17th century by the architect Ferdinando Tacca still preserves a magnificent and elegant Manneristic staircase, which is even earlier that the prepytery, designed by Bernardo Buontalenti (1574) and transferred from the church of Santa Trinita.

The museum is arranged on three different levels and gives access to a small cloister with a Renaissance well, where the cells of the monks opened. This was the seat of the Agostinias from the congregation of Lecceto from the 16th to the 18th centuries.

The exhibition highlights some extraordinary masterpieces of Italian art like the "Madonna" by Giotto that was originally located in the church of San Giorgio alla Costa, The "Adoration of the Magi" by Paolo Uccello and "St. Julian" by Masolino; besides displaying a well-assorted and precious series of liturgical objects and vestments, which includes also a very expressive polychrome plastic.