The 12th March 1326, with a solemn celebration, the first stone of the new and larger church of Saint Francis was laid. Designed by two Sienese architects, Agostino di Giovanni and Agnolo di Ventura, the church was erected in same the place where the previous and smaller Franciscan church, which was initially preserved in order to enable the continuity of religious practice, used to stand.
After little more than twenty years from the opening of the building yard, the onset of the terrible Black Death of 1348 struck the city tremendously, killing over half the population. This brought not only the construction of the church of Saint Francis, but also other construction sites in the city to a standstill. At that time the apse and the crossing chapels had almost certainly been completed as, together with the altar, they were always the first elements to be constructed in a church. Some fragments of frescoes that are visible on the right side wall of the nave can be traced back to this period: they represent the Visitation, some Saints and The Stigmata of Saint Francis. The fake polyptych painted by Andrea Vanni in the chapel of the Sacrament, also belongs to the same period (1370).
The construction of the church was resumed in 1407. The restoration work was particularly active and much needed after the long period of neglect. It is easy to believe that this new building zeal had been ignited by the presence of St. Bernardino of Siena, who lived there and certainly wished to see the completion of the great church dedicated to Saint Francis.
The influence of another great man from Siena, Pope Pius II, was responsible for the inclusion of the new church of Saint Francis within the new city walls which were built in 1473 and are still visible in the steep valley behind the apse. Pius II had a deep bond with the Franciscan church: as well as having had buried his parents there, he had personally spent some time in the friary of the Friars Minor. The building was completed in 1475, although a few years later, in 1482, the great Sienese architect, painter and sculptor
Francesco di Giorgio Martini was asked to raise the side walls to give greater proportionality to the building. On that occasion the artist also created the magnificent main portal, which currently stands in the church, to the left of the entrance.
The current building, despite a number of alterations made throughout the ages, still maintains the traditional layout found in the churches of the Mendicant Orders: a vast and plain single room, without columns which could distract the faithful from the preacher’s words; the transept, divided into chapels, is inserted into the end of the great nave. It has the same Egyptian cross floor plan as the church of San Domenico in Siena. Both buildings, entirely built with bricks, are clear examples of the message of the Mendicant orders: do not impress with splendour, but stir the souls through word and example.