The narrative begins with the Annunciation at the top left, where the Virgin Mary learns from the Angel Gabriel that she is to bear God's son. Below, she appears enthroned with the infant Christ, while in the central panel she grieves along with Saint John the Evangelist at the Crucifixion. On the right, the adult Christ and the Virgin sit enthroned, while above Saint Francis, regarded as the second Christ, receives the wounds of Jesus' crucifixion, known as the stigmata. Saint Francis' presence here, among images depicting the life of the Virgin and Christ, suggests that this triptych was commissioned for a Franciscan patron.

In planning the composition, Duccio has created an innovative system of internal perspective, to counteract the fact that the folding wings of the triptych would have been viewed at an angle.  This can be clearly seen in the architecture of the Annunciation scene, which is built upon a diagonal axis.