From the lower church a spiral stairway leads to St. Gregory's Chapel. The paintings in this chapel, as also those of Conxolus, are very important for the study of medieval roman art.
On the right of the window is the famous fresco of St. Francis of Assisi, depicted without the halo and without the stigmata, with the inscription, Fr. Franciscus; therefore it was painted while the Saint was still living, before 1224, the year in which he received the stigmata.
The fresco has a magnificent simplicity which reveals with remarkable vividness, the humble and serene spirit of the great Saint of Assisi. On the left is depicted Cardinal Ugolino, bishop of Ostia and afterwards Pope Gregory IX, consecrating this chapel. Many hold that near Ugolino is St. Francis who would therefore have been present at the consecration of the church. Below the fresco is the inscription: " Hic est Papa Gregorius, olim episcopus hostiensis, qui hanc consecravit Ecclesiam". And lower down : " Pontificis Summi fuit anno picta secundo- haec domus".
On the right of the window is St. Michael the Archangel with a thurible in his hand; above the window, the Apparition of the Angel to Fra' Odo; above the altar is the Crucifixion with Longinus and the Virgin on the right and Steaton (sponge-bearer) and St. John on the left. In the small apse there is the Saviour Blessing and on the sides St. Peter and St. Paul; on the vault the Four Animals, symbols of the Evangelists and Four Cherubim.
On the right of the altar is the head of St. Onofrius. All these paintings were done by Roman-byzantine painters, a school which goes up to the beginning of the XIIIth century. The ex-voto on the right of the window is a work of the XVth century, perhaps by Antoniazzo Romano.