Fioravanti organized the altar part of the cathedral in a more complex way. To place the three formerly existing side aisles, included in the architectural composition of the altar premises, he had to divide the side naves in half and complete them with four apses. The prothesis and the Petropavlovskiy side-chapel are located in the northern part of the altar. The southern part houses the diaconicon also serving as the Eulogy of the Virgin side-chapel, as well as the St Demetrius of Thessaloniki side-chapel. They are separated by the rather low walls, about four meters high, and are illuminated through the windows of the eastern cupolas and side apses.
The frescoes in the chancel were discovered during the restoration in the late 19th-early 20th centuries. The wall-paintings of the Petropavlovskiy (of SS Peter and Paul) side-chapel and the Prothesis illustrate the Seven Sleepers of Ephesus, the Three Hebrews in the Fiery Furnace and The Forty Martyrs of Sebaste scenes. The vault and the walls of the Eulogy of the Virgin side-chapel depict the Eulogy of the Most Holy Theotokos, the Adoration of the Magi and the Nativity of St. John the Precursor. Those paintings could have been made by Dionysius. Nowadays they are hidden behind the iconostasis.