The foundation stone of the large basilica for housing the remains of St. Francis was laid on July 17th, 1228. The complex was constructed in a very short time thanks to the intervention by the papal court. After just 22 months, the saint's body was buried in a dedicated cell dug under the main altar of the lower church, in practice reserved for the devotion of the pilgrims for the humble friar, whilst the upper basilica, dedicated to Mary, acquired the status of a papal chapel.
On 25th May 1253, Pope Innocent IV solemnly consecrated the altars of both churches and at his solicitation, notwithstanding the Order’s charter and despite the opposition by the minister general of the Friars Minor, the decoration of the complex began, of an absolutely exceptional nature in respect of the Umbrian and Italian context.
In the upper basilica the decoration, which includes twenty-eight panels with Stories of St. Francis, is the most complete and exhaustive image biography of the Saint. This decorative undertaking should be placed during the pontificate of Pope Nicholas IV, between 1288 and 1292, when the Franciscans were allowed to use the substantial alms collected here for decorating the church. There is nowadays a consensus of opinion in recognising the Roman Jacopo Torriti as the creator of the decorative plan and the initial work in the nave; he was flanked by a rota of at least four maestri, among whom the young Giotto, who in the middle of the cycle adopts compositional solutions developed a decade later in the Cappella degli Scrovegni in Padua, stands out.