In the 17th century, the state-owned Ovchinnaya sloboda was located in the area of Zamoskvorechye, which dealt with wool and sheepskin. This is recalled by the names of Runovsky and Ovchinnikovsky lanes, as well as the stone chambers and the Church of Archangel Michael.

The stone building of the church was erected around 1662. The bell tower with an octagonal ringing tier and the refectory were added around 1700. At this time, the windows of the apse were adorned with frames in the style of Moscow Baroque, featuring columns and scrolls in two tiers, topped with six-pointed Orthodox crosses. If you look closely, you can see images of a skull and bones under the crosses, symbolizing the 'Head of Adam'.

Architectural studies show that the church originally had three domes, but two were later removed due to dilapidation. There was also a 'hill' of kokoshniks under the domes, which was lost due to changes in the church's ceilings. Despite its name, only the southern chapel is consecrated in the name of Archangel Michael, while the main altar is dedicated to the Protection of the Mother of God. Later, in 1770, the chapel of the Holy Martyr Haralampius was consecrated.

In the early 1930s, the church was closed. Its walls were successively used for offices, a bakery, a dormitory, and it also served as a utility room. In 1955 and 1961, the church was separated from the Middle Ovchinnikovsky lane due to the construction of an administrative building on Sadovnicheskaya Street, designed by architects G.I. Grigoriev and T.V. Vladimirov. The interior decoration was completely lost, but two icons, one of which was painted by the famous icon painter Simon Ushakov in 1652, were transferred to the Tretyakov Gallery and thus preserved. In 1998, services resumed in the church, and restoration was carried out.