The apse was frescoed by Benozzo Gozzoli in 1452 and is entirely covered with Stories from the Life of St Francis, other Saints and members of the Franciscan Order. Having previously collaborated with Beato Angelico, these frescoes are the first extraordinary example of Gozzoli's achievement of the "status" of independent master.
Today, this cycle of frescoes, which survived the 1997 earthquake, appears in a state of full legibility, thanks to the masterful restoration work completed in 2000.
The frescoes were commissioned by Fra Jacopo Mactioli da Montefalco, prior of the monastery. The twenty episodes from the Life of the Saint are narrated in twelve scenes arranged in three registers, with the narration moving from left to right, starting from the bottom. The vaults of the apse are decorated with plant elements, figures of Franciscan Saints and the Glory of St Francis. In one of the episodes, Gozzoli depicts St Francis blessing the town of Montefalco: the rural background reflects the importance of the cultivation of vines for the town. Also, in the apse of the church he perhaps alluded to the local wine, Sagrantino, by painting bottles of red wine on the laden table of the Cavalier of Celano.

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