Numerous wall depictions may be seen in the great basilica, or in the numerous chapels of the area. Two of the most important were executed in the encaustic technique (using wax as the medium for the pigment) and painted on the sixth century marble panels, to either side of the Holy Table. The mural on the left depicts the sacrifice of Isaac. Abraham is shown at the moment when he was about to slay his son, and an angel of the Lord commanded him to stop, in that he had proved his faith, but a ram caught nearby would be offered in sacrifice instead. The mural on the right depicts the sacrifice of Jephtha’s daughter. These depictions of sacrifice taken from the Old Testament would appear to have been added in the seventh century as a way of expanding the iconographic program of the apse, and pointing towards the fulfillment of the sacrifices of the Old Testament with the sacrifice of Christ, celebrated at each Divine Liturgy on the Holy Table in the centre.

The Chapel of Saint James is adorned with a fresco that has been dated to the middle of the fifteenth century. This shows the All-holy Theotokos of the Batos, with the Burning Bush depicted on her garments. To her left is Saint John Chrysostom, and to her right, Saint Basil and Saint James, First Bishop of Jerusalem. Liturgies attributed to each of these three are celebrated in the Orthodox Church. To her far left is a depiction of the Prophet Moses. Above, Christ gives the Law to Moses, and the Gospel to the Apostle.

The monastery refectory has also been adorned with frescoes. The earliest date from the thirteenth century, and show the Prophet Elias being fed by a raven, and Saints Anthony and Paul breaking bread together. A depiction of the Second Coming of Christ below dates to 1573, while the Hospitality of Abraham was added in 1577.

Very little of the monastery was plastered before the eighteenth century, and that is why there are so few frescoes. When the walls of the basilica were plastered in the eighteenth century, they were not painted, but instead, the large icons that had adorned the walls before were simply returned to their places.

In the south wall of the monastery there is a small cubicle built into the wall, called the Chapel of the Holy Cross. This contains simple decorations simulating the grain of marble, and dates perhaps from the seventh or eighth centuries. In more recent times, many of the chapels of Sinai were decorated with geometric motifs and simple depictions of saints in a secco technique by Father Pachomius, who died in 1958.