The Archangel Cathedral was first adorned with murals in the reign of Tsar Ivan the Terrible in 1564-1565. In the early 17th century, during the Polish-Swedish invasion, the murals of the cathedral were damaged badly. It was decided to restore it. The work was in progress from 1652 to 1666. According to the order of Tsar Alexis Mikhailovich, the new wall-painting was to be like the ancient one. Before the beginning of the work, Stepan Rezanets, maker of the Armoury Chamber, with his assistants made descriptions of depictions that survived in the cathedral, marking their locations. The Tsar's decision gives evidence to the point that the program of the murals were urgent in the reign of Romanovs.
The new murals were created by a big team of makers from various Russian towns – Yaroslavl, Rostov, Kostroma, Vologda etc. The team was headed by Simon Ushakov, illustrious royal painter. Together with Simon Ushakov there worked such talented makers as Fyodor Zubov, Sidor Pospeev, Yakov Kazanets, Iosif Vladimirov and others. They brought to ancient compositional schemes refined drawing, complicated architectural framing of compositions, bright and festive intensive blue, cherry, yellow, white, pink and pistachio colours.
The idea of "political theology" of the time of Ivan the Terrible is closely interwoven with the themes of death and confession. The "Epigraph" of the whole wall-painting is the frescoes of the loggia over the entrance to the cathedral illustrating the chronicle about adopting Christianity by Prince Vladimir. In the altar part there is a theme of the triumph of Russian National Church. Here is the composition of Sophia Wisdom of God surrounded by the images of Russian hierarchs.
In the central dome there is composition "The Paternity". The western wall and a part of vaults are covered with a series of compositions dedicated to the Symbol of Faith (short summary of main doctrines of the Christian faith). It continues the theme of choosing the religion, started in the loggia, and is a reminiscence of the idea of protection of the faith as a duty of principal and royal power. A part of the Symbol of Faith circle is "The Judgment Day" composition covering a part of the western wall.
On the northern and southern walls of the cathedral there are compositions telling miracles of Archangel Michael, the highest angel and guide to the world of God's Will. In Russia he was traditionally worshipped as Great Princes' patron and angel to guide souls of the dead to the throne of God. The theme of glorification of the royal power is accompanied by depictions of saint princes – royal relatives and saint warriors, their protectors. Among them are Vladimir and Olga, Boris and Gleb, Peter and Fevronia of Murom, Prince Michael of Chernigov and his Boyar Fyodor.
Unique feature of the Archangel Cathedral's murals is series of tombstone portraits of princes of Moscow dynasty. They are located right over princes' burial places. The burial place of Tsar Ivan the Terrible is adorned with frescoes as well.
Frescoes of the Archangel Cathedral were often replaced with new layers of oil painting. In 1950-s, they were open from under multitudinous layers by a team of artists of Palekh. In 1978-80, murals were strengthened and some new sections were opened.