In 1365, eight years after the foundation of the Chudov Monastery, Metropolitan Alexius built a stone church in the name of the Archangel Michael, probably in the place of the former wooden church. The cathedral was built and consecrated in one year, which testifies to the small size of the construction. The white stone temple was painted and richly decorated with icons and other ecclesiastical attributes. It is possible that at the beginning, or soon after its completion, a side chapel of the Annunciation was being joined on its south side, for according to the chronicle, Prince Dmitry ordered to bury the Metropolitan, who died in 1378, "in the church built for him near the Holy Altar on the right side in the Church of the Annunciation". The depiction of the cathedral of 1365 on the margin of the icon of Metropolitan Alexius gives an idea, where the temple is shown with three arched gables (zakomary), apparently four pillars, with a massive dome, without a basement, standing directly on the ground, and with a side chapel on the south side.

According to the "Life" of St Alexius, written in the middle of the 15th century, in 1431 the vault of the temple was "...very much collapsed from dilapidation", the destroyed church was demolished to the ground and soon completely rebuilt. According to the same narrative, the rebuilt cathedral was smaller than the original metropolitan's temple, but taller because it was built on a two-storey basement, "...high and spacious and beautiful and triple-domed…" It also mentions the construction of a stone refectory by Metropolitan Alexius.

Cathedral of the Miracle of the Archangel Michael at ChonaeIcon of Metropolitan Alexius with Life Scenes

By the end of the 15th century the Church of the Miracle of the Archangel Michael had fallen into dilapidation, probably it happened after the fire of 1493, and in 1501 Grand Prince Ivan Vasilievich ordered it to be demolished and a new one built on the same site. The construction was completed in 1504. There is reason to believe that the new church preserved the lower white stone part of the 1431 building, as the newly created brick volume, similar to the former building, was placed on a two-storey white stone basement. Unfortunately, the cathedral, which existed until 1929, has not been sufficiently studied, so it is not possible to prove the inclusion of the old temple's basement in the new construction.

The layout of the new brick cathedral was 13.7 x 18 metres. Three apses adjoined the almost quadrangle from the east. The drum of the single central dome allowed light to pass through. It rested on braced arches set between four square pylons. The cathedral had three entrances, decorated with perspective portals in white stone, to which high staircases with porches led. The façades were divided by pilaster strips into three curtain walls and finished with semicircular arched gables (zakomary).

The author of the construction is unknown, but the decorative techniques used in the monument suggest the possible involvement of Italians who worked in the Kremlin in the late 15th and early 16th centuries. An arcaded frieze on columns encircled the cathedral almost under the arched gables, and a similar decoration adorned the drum. The cornices were decorated with patterned terracotta belts, the ornamentation of which is characteristic of the Italian Renaissance. The lower basement was dark, while the upper basement was lightened by windows. Despite its small size, the temple appeared majestic and solemn.

Cathedral of the Miracle of the Archangel Michael at ChonaeIconostasis of the Cathedral of the Miracle of the Archangel Michael in the Chudov Monastery

The "Kremlenagrad" map of the early 1600s shows the cathedral already five-domed with a porch on the south side and a high flight of stairs on the north side. The four corner cupolas were added later on top of the vaults, and had no windows. Probably in the 17th century, the cathedral was surrounded on three sides by a closed porch. According to the inventory of 1763, the temple was connected with the Church of the Annunciation and the archbishop's quarters by covered stone passages with a bell tower to the west of the cathedral. In 1778 the cathedral was restored during the period of Metropolitan Platon. In the middle of the 19th century the iconostasis and the wall paintings from the 16th century were renewed. In 1893-1894 the restoration of the cathedral was carried out under the supervision of the archaeological commission, during which the single-domed church was reconstructed and the five-tiered iconostasis was restored in the "ancient style".

In 1918 the monastery was closed, but its buildings were preserved until 1929, when the Cathedral of the Miracle of the Archangel Michael was demolished together with other monastery buildings for the construction of the Military School named after the All-Russian Central Executive Committee.