The Upper Church is the highest building of Sacro Speco and was the last part of the shrine to be built. It is divided into two irregular spans, consequence of the several alterations made to its structure.
The first span, near the entrance, is rectangular and much higher than the other one; they are separated by an arch, above which there is the fresco of the Crucifixion. The first span presents a transversal arch and a first cross with groins, while the second span shows a much lower cross, without groins. The apse is bored through rock. Some steps lead to the transept.
Every available room is frescoed, which partly hides the inconsistencies of the building. A considerable inconsistency is the location of the pulpit, which is at the back of the church, behind the believers. The most reliable theory is that at the beginning the upper church might have consisted only of the room of the first span, with the entrance and the pulpit on the opposite wall. The most ancient rooms, once excluded, might then have included and the wall, where today there is the arch with the Crucifixion, was demolished.
The vault of the first span might have been elevated and it would have been divided into three equal rooms if the works hadn't stopped (the reason is not known), so that everything has remained has it is today.
The first part of the Upper Church is a XIVth-century adaptation of another building of the first half of the XIIIth century, of which remain the pulpit adorned with large roses and a eagle supporting a bookstand on its wings: in this part all the frescoes are of the school of Siena (XIVth cent.). In the wall in front is the biggest painting: the Crucifixion. "The most outstanding of all the figures is that of Christ Crucified, which heartfelt devotion and a good knowledge of the truth".
On the left is a group of pious women, dressed in white, with Mary, the Mother of Christ. Mary Magdalen with a red dress and fair hair is at the foot of the Cross; on the right is the centurion. Lower down the soldiers draw lots for Christ's garment. An Angel holds within its arms the soul of the repentant thief, and a horrible devil violently snatches that of the impenitent thief from his mouth. The wall on the right of the entering pilgrim is divided into three sections. In the lower section is the kiss of Judas, the flight of the Apostles and the Scourging. In the middle section can de seen Christ being condemned to death and His Journey to Calvary; this scene is very interesting for the number of persons, the liveliness of the representation and the richness of its details. A crowd of men, in various styles of dress, on foot and on horseback, below the walls of Jerusalem, represented as a medieval city with towers and battlements, walks behind Christ and Calvary. In the background can be seen some flags with a black dragon and the half-moon. Christ, bearing the Cross, follows the two thieves. "The Saviour's sorrowful head which turns with a tired and affectionate gesture to look at His Mother, has been depicted with very little skill but with much love". In the highest section, beneath the vault, is the Descent of the Holy Ghost.
On the vault are depicted the Four Great Doctors of the Latin Church, sitting on gothic thrones on the high backs of which are the Evangelists. The wall on the left is also divided into three parts. In the higher part there is Christ's triumphant entry into Jerusalem on Palm Sunday. "Note the group of children, especially that small plump child who is comfortably seated and playing his trumpet. In very few paintings of the middle Age can be found a more vivid and more beautiful scene. It is really a picture taken from the life of children and reproduced with great sentiment and skill".
Then there is an Angel, seated on the empty sepulchre, announces Christ's Resurrection to the pious women the Three Marys at the Sepulchre; In the middle section Christ appears to Mary Magdalen. "The fresco really gives the impression of a beautiful frosty morning". Then there is the scene of St. Thomas who touches Christ's wounds. Above it is Our Lord's Ascension.
In the second part of the Upper Church, with a somewhat lower vault, are paintings which go back to the beginning of the XVth century. In the fresco in a bad state of repair, on the wall in front, St. Benedict is depicted in pontifical garments, sitting on a throne beside Saints and members of the family of his origin. The pictures on the left wall have been almost completely ruined by the humidity of the rock.
However those on the right wall are in good condition and represent the attempt on the life of St. Benedict by the monks of Vicovaro and the cure of the lazy monk who used to leave the oratory while his brothers remained there in prayer, and whom St. Benedict cured by striking with the rod.
By climbing all the steps up to the High Altar, one arrives at the Transept where the frescoes are of the school of Umbria. These steps were built during the restaurastion of the 1853, in order to join the transept with the two spans.
On the right is the last conversation of St. Benedict and St. Scholastica. The fresco depicts the moment in which, in answer to St. Scholastica's prayer, it begins to rain heavily and St. Benedict is thus compelled to stay with her throughout the whole night.
On the other side is St. Benedict in the Tower at Montecassino watching his sister's soul fly to heaven under the form of a dove. In the two small chapels are badly damaged paintings depicting St. Scholastica's death, St. Maurus' death and the beheading of St. Paul.
On the second arch is a beautiful paintings of St. Agnes, wearing a white dress and a veil on her head. The two frescoes in the lunettes represent St. Placid's martyrdom near Messina; and the miracle of St. Peter and John near the beautiful gate of the temple: the cripple can be seen both before and after the miracle. The small window with the beautifully coloured glass depicting Our Lady and the Divine Child is a XVth century work.