Half a century after Martin was deposed, Pope John VII, who reigned for just two years between 705 and 707, had one of the two chapels on either side of the church's apse frescoed. The images depict a group of Egyptian physicians who were not allowed to charge their patients for their cures. They were originally pagan medicine men until co-opted by the Bishop of Alexandria sometime in the seventh century. In the frescos, they are given the attributes of traditional Christian saints, including halos. Between them is an image of Christ, who is depicted, unusually, with a large and thick beard. These pictures were thought to have prodigious powers to cure diseases. Sick people who were beyond hope of any other remedy spent the night in front of them awaiting a miracle. Presumably, some did indeed enjoy a miraculous recovery: this is the only part of the church that seems to have been used after the earthquake buried it. 

The artists themselves were probably from the Eastern Mediterranean. The inscriptions identifying the saints are all in the Greek alphabet, and the plaster was mixed with straw rather than sand, which was a characteristic of painters from the Near East.

Forty years later, between 741 and 752, the chapel on the other side of the apse was decorated — but this time the artists were probably from Rome, or at least Italy, rather than from the East. The inscriptions are in Latin, not Greek: one of them, instead of giving the figures a name, as is usual, disarmingly describes the image of four saints as being of "sanctus ignotus". The pope at the time was Zacharius, but the man who paid for the paintings was Theodotus, who was Zacharius's ambassador to the Franks.   Theodotus ensured that he was depicted on the chapel's west wall, with his wife and two sons, next to the Virgin and infant Jesus. 

The centre of the chapel is an extraordinary fresco of the crucifixion, in which Christ, dolefully staring into the distance, is depicted fully clothed rather than naked. There are also pictures of grisly martyrdoms, including that of St Quiricus, who was only three years old when he was killed with his mother during the persecution of Christians ordered by the Roman emperor Diocletian. They underwent various horrible tortures together, including being whipped, having nails hammered into their heads, and boiled in a cooking pot, all of which they survived, before the infant Quiricus was finally killed by being smashed against marble steps. His mother was decapitated. It is all lovingly depicted on one of the walls of the Chapel of Theodotus.