Along the side aisles there are ten chapels, five on each side, included in the original design of Alessi.

From the end of the 1500s the Franciscans of Santa Maria degli Angeli began to assign the use of the chapels to those who requested them according to the custom which had become widespread over the centuries.

It was not only the aristocracy and middle class but also municipal institutions and confraternities which requested that the chapels be conferred upon them, in order then to decorate them as a tangible sign of their personal devotion to St. Francis and to the Mother of God as well as an indication of their social status and their own artistic tastes.