The Church of St. Francis was consecrated in 1291 and was originally a Gothic building, typical of the mendicant order, with a single nave. Some elements of the original building remain, such as the exterior of the apse, the right side and some windows. In the following centuries, renovations and expansions were made. Most important is the complete renovation that took place between 1707 and 1727 and gave it its current late Baroque appearance.
The stucco work is by Antonio Milli from Tiferna, while the painter Lucantonio Angiolucci from Città di Castello decorated the medallions of the vault with Saint Francis, Saint Anthony and Saint Joseph of Cupertino. The choir stalls, depicting the lives of Mary and Saint Francis, decorated with graffiti and ink inks and dated to the first decades of the sixteenth century, are attributed to the same craftsmen who worked in the cathedral's wooden choir. In the church there is a reproduction of Raphael's "Marriage of the Virgin", the original was stolen by Napoleonic troops and is currently in the Brera Art Gallery.