The description of the monastery from 1714 mentions that the church housed a five-tiered iconostasis and numerous icons, "painted with gold and colors." The interior decoration of the church can be judged by a description compiled in 1763 by Peter Svinin. Among the many icons, three images of Saint Euphemia stand out, adorned with silver covers and gilded crowns; above the door to the hospital cells was the image "Fatherland" in a gilded frame.

Throughout the 18th century, the church underwent multiple repairs. Due to a lack of funds, Hieromonk Philaret appealed to Princess P.I. Golitsyna, whose mother was buried in the hospital church, asking for donations to replace the roof. In 1765, the roofs over the altars were repaired, and the tent was repaired multiple times. In 1793, a major renovation was carried out: the tent was re-roofed, the brickwork was restored, and the walls were plastered. The interior of the church was also renovated, and a new iconostasis was installed. A contract with the serf goldsmith of Count N.P. Sheremetev, Ivan Timofeevich Serkov, who gilded the new iconostasis, has been preserved. At the same time, the hospital cells were also rebuilt.

During the renovation work on the southern wall of the refectory part of the church, fragments of the walls of the original volume of the church from the early 18th century were discovered. However, the updated church stood for a short time. In 1805, the question of its repair arose again, but the condition of the building required more serious measures. Funds for the dismantling of the church and the construction of a new church were donated by Anna Alexandrovna Golitsyna, the wife of M.M. Golitsyn. She wished to arrange a burial place for the Golitsyn family in the new church and consecrate it in the name of Archangel Michael, the patron of her husband. The project was executed by Ivan Vasilyevich Yegotov, who also built the main house in the Golitsyn country estate in the village of Vlakherskoye (Kuzminki). The works of this architect became known in classical architecture in Moscow, including the main building of the military hospital in Lefortovo and the main house in the estate of the Durasovs in Lyublino. Since 1803, he had been the director of the Kremlin drawing expedition.

The church is built in the classical style of "Alexander Empire" and represents a cubic volume with a dome on a wide drum. A feature of the church's architecture is its eastern facade, the apse of which is equal in height and width to the church, reminiscent of rotunda mausoleums popular in the late 18th century. The main entrance to the church, established during the Soviet era, was marked by a solemn portico with elements of the Tuscan and Doric orders. The architrave made of white stone is decorated with stucco rosettes, and the tympanum of the pediment symbolizes the "all-seeing eye." During the construction of the new church, the western wall, which was the wall of the hospital cells, was preserved. Inside the church, in the northwestern part, a white stone staircase was made leading to the burial place. The church was consecrated in 1809 by Archimandrite Viktor of the Don Monastery. From a description of the 1820s, it is known that the roof of the dome and the church was covered with sheet iron, and the cross was gilded.

The church in the name of Archangel Michael became the burial place of the Golitsyn family, and by 1822, there were thirteen tombs. In 1845, a new iconostasis was made, and in the 1860s, wall paintings in the church and altar were mentioned for the first time. The entire church was painted in 1877 by artist M.E. Golovanov, preserving the paintings from the 1860s. The monumental painting in the refectory part of the church was updated by icon painter P.M. Sokolov from the village of Palekh in 1894-1895.

Prominent representatives of the Golitsyn family are buried in the tomb. Here, under cast-iron slabs, rests the ashes of N.P. Golitsyna (born Countess Chernysheva) and her husband V.B. Golitsyn. According to contemporaries, A.S. Pushkin depicted Natalia Petrovna as an old countess in "The Queen of Spades," and the plot was told to the poet by the princess's grandson. Her son, Dmitry Vladimirovich (1771-1844), who was the Moscow governor-general for over 20 years, a participant in the Patriotic War of 1812 and the foreign campaigns of 1813-1814, a knight of almost all Russian orders, and a member of the State Council, is also buried here. Next to him rests Tatyana Vasilyevna Golitsyna (born Princess Vasilchikova), a stately lady and wife of D.V. Golitsyn, known for her charitable activities. Here lies the ashes of another hero of the 1812 war, Lieutenant General Prince Nikolai Yakovlevich Golitsyn. In total, there are more than 30 burials of representatives of the Golitsyn family in the church.

In 1893-1894, repairs were carried out on the facades and interiors of the church. The need for repairs was caused by the dilapidation of the interior. The monastery brotherhood reported that "the plaster in some places had cracked, the iconostasis had darkened, and the painting, both on the icons and on the walls and vaults, had deteriorated and become dirty, the floor, where white stone was laid, had become uneven." Learning about the repairs, Prince S.M. Golitsyn appealed to the Synod Office with a request to allow repairs at his own expense, making the entrance to the tomb from the street, and decorating the entrance from the church in the form of a marble arch with a carved door, proposing to widen the existing staircase.

In 1894, according to the project of architect M.P. Ivanov, stone vestibules were added to the northern and southern facades, and a narthex and new porch were arranged in the refectory part. The vestibule at the portico of the northern entrance to the church was dismantled in the 1950s during restoration work, and the northern portico was restored at that time. In the summer of 1894, contractors were found: icon painting work was carried out by I.M. Frolov, painting and decorative work by painter P.M. Sokolov from the village of Palekh, and carpentry and joinery work by S. Fomichev. Within a year, a new iconostasis was made "with the addition of a new tier above the local icons." In the refectory, two iconostases were also installed "of the same design as the pre-altar one, and gilded entirely with red gold." On the middle pillar and walls of the refectory, "16 sacred images in the Frieze style with gold" were repainted. At the same time, all window frames and doors were replaced, new marble window sills were made, and the floor was laid with Podolsk stone (sandstone). The interior decoration of the church has been preserved fragmentarily.

Since the 1930s, the church housed a department of the Architecture Museum, where memorial monuments were collected: sculptural tombstones from the churches of the Don Monastery, other Moscow monasteries and churches, as well as from suburban estates. For many years, the department of memorial plastic and sculpture of the State Research Museum of Architecture was located here. Only in the mid-1990s, after the removal of museum exhibits, restoration work was carried out in the church. The restorers revealed the paintings in the main part of the church and in the refectory. On the western wall of the refectory, the composition "Sermon on the Mount," created in 1895, was uncovered.

Currently, the church preserves memorial sculptures from the churches of the Don Monastery and the Golitsyn tomb, as well as memorial tombstones over the burials of representatives of the Golitsyn and Shcherbatov families, and tombstones transferred from the Small Cathedral. In 2017, restoration work was carried out: the reconstruction of profiled plaster panels on the walls of the tomb, painting of walls and vaults, restoration of icons, fabrication and installation of an altar in the sanctuary, strengthening of the paint layer, and restoration of lost paintings. All heating devices were also replaced with the laying of new pipes under the floor slabs and the installation of a new thermal input under the porch of the portico. Lightning protection of the building was carried out. In 2017, the Church of Archangel Michael became a laureate of the Moscow Government competition for the best project in the field of preservation and popularization of cultural heritage sites "Moscow Restoration."