The museum complex, modified by a series of restructurings from the 17th to the 19th century, has recently been renovated (2024).  A group of  carefully designed spaces for exhibits was created, including the Archaeological and Via Francigena Museum, the Spezieria di Santa Fina, and the Raffaele De Grada Gallery of Modern and Contemporary Art.

The Archaeological and Via Francigena Museum contains archaeological artefacts and other important items of cultural heritage from the city and the surrounding area, which illustrate the material history of San Gimignano from Prehistory to the early modern age.
The museum also documents the evolution of table and kitchen equipment, and variations in their manufacturing techniques, with ceramic and glass finds from the period between the Middle Ages and the Renaissance. A special section on the link between San Gimignano and the Via Francigena describes the architectural evolution of the city with reference to the arterial road’s importance in the Middle Ages. The displays, including the bronze offering statue called Hinthial (in its setting) and artefacts from the archaeological site of the late-ancient Roman Villa of Aiano, illustrate notable aspects of how the population grew in the area along the Via Francigena in the Etruscan and Roman eras.

The Spezieria di Santa Fina is a city institution that was first documented in the early sixteenth century; it was annexed to the hospital of the same name that dates back to the second half of the thirteenth century.
The rooms recreate the original layout and aromas of the pharmacy, one of the oldest in Tuscany, with the division between the kitchen, where medicines were prepared, and the shop, where the products were sold in valuable ceramic and glass vases that can be dated to between the fifteenth and eighteenth centuries. The museum includes a display of ancient furnishings and “medicines”, and some of the ingredients used to prepare the medicines.

The Gallery of Modern and Contemporary Art was named after Raffaele De Grada. It holds paintings from nineteenth-century Tuscany and some Italian twentieth-century “masters” as well as contemporary works of art. Special sections document views of San Gimignano from the eighteenth to the twentieth centuries, works by the painters Raffaele De Grada and Giannetto Fieschi and local twentieth-century artists, important donations and the Environmental Art projects Affinità and Arte all’Arte.