The church dedicated to St Michael Maleinos, the patron saint and the namesake of the first Russian Tsar of the Romanov dynasty, originally existed in the monastery as a side-chapel to the Ascension Cathedral. The saint came to be known as "Maleinos" from the mountain on Athos where he spent his ascetic life. The side-chapel, first mentioned in 1617, was probably built by the mother of the young Tsar Mikhail Fyodorovich, nun Martha (secular name Ksenia Romanova), who settled in the convent in 1613. Written sources mention a wooden church of Michael Maleinos in 1618. It is possible that the great aged nun built a side-chapel of St Theodore "i.e. in Perge" in honour of the angel of her husband Feodor Nikitich Romanov (from 1619 – Patriarch Philaret). The earliest recording of this side-chapel is dated 1626.

In 1634, three years after the death of nun Martha, Tsar Mikhail replaced the wooden church with a stone one in a single summer. It was built to the north of the Spasskiye (Saviour's) Gates, with the altar part adjoining the fortress wall. The new temple was built by Bazhen Ogurtsov and Semeika Beloy – apprentices in stonemasonry. The bell tower was probably built in 1694 when the church was rebuilt. At the same time the side-chapel of St Theodore of Perge was consecrated.

The two-storey building had a kitchen with cellars on the ground floor, a church on the first floor, a bell tower, and a common refectory. The high quadrangle chapel ended with a four-slope roof with a small dome on a deaf drum. Three lowered apses were right against the fortress wall. A refectory adjoined the church from the west. The decoration of the building was typical for the Moscow Baroque architecture of the 17th century. The increased volume of the church was emphasised by paired three-quarter columns. Under the roof of the church, a series of profiled corbel arches rested on columns, which were cut by a complex cornice. Window openings on the second floor were framed by columnar surrounds with broken triangular pediments. There was a richly decorated octagonal bell tower above the refectory in the north-west corner of the church. In its decoration, columns similar to those in the temple were used to accentuate the corners of the facets. Above the open-arched tier of the bell tower was a smaller octagon with small arched windows in rectangular niches. The octagonal tier was surmounted by triangular frontons, above which was a dome on a faceted drum. A covered porch with stairs leading to the second tier was attached to the northwest corner of the building. To the south of the church there was a household yard that was accessed from under the church along the wall of the fortress. Wooden gates closed the passage.

Plan of the Ascension ConventView from the south on the churches of St Catherine (left), St George (centre), St Michael Maleinos with bell tower (right) of the Ascension ConventChurch of St Michael Maleinos with bell tower, west façadeChurch of St Michael Maleinos with bell tower, south façadeView from above on the Church of St Michael Maleinos of the Ascension Convent

The church had a special patronage of the first tsars of the House of Romanov and received many valuable donations.

The Church of St Michael Maleinos and its side-chapel were badly burned in the Moscow fire of 1737 but later rebuilt.

In 1808, an old white-stone sculpture of St George, made in the 15th century to decorate the Spasskiye Gates, was placed in the church as an icon. After being removed from the tower, it was first kept in the Church of St George, built in 1527 by Basil III to the south of the Ascension Convent and later transferred to the Convent's administration. The dilapidated Church of St George was demolished in 1808 for the construction of a new Church of St Catherine, and the statue of St George on horseback was transferred to the Church of St Michael Maleinos.

By decision of the Soviet government, the Church of St Michael Maleinos was dismantled along with the entire monastery in 1929. St George – a unique example of ancient Russian stone sculpture was broken during the destruction of the monastery. Now a fragment of the upper part of St George’s figure is exhibited in the Tretyakov Gallery.