The Church of St. Sergius in Krapivniki has been known since the late 16th century and is depicted on the "Peter's Map" of Moscow, which is the only evidence of the existence of a single-domed church at that time. The first written mention of the church dates back to 1625, when it was wooden.

The name "in Krapivniki" has several versions of origin. One suggests that the name is related to a sparsely populated area overgrown with weeds and nettles. Another version links it to the name of the owner of one of the courtyards in the alley where the church stands.

In 1752, near the church was the estate of college assessor Alexei Krapivin. The church was also called "in Old Silverniks," "by the Pipe," and "in the Watchmen." Before the revolution, it was the only church in the center of Moscow, whose main altar was consecrated in honor of St. Sergius of Radonezh.

The Sergius Church is small, located at an angle to Krapivenka Alley, and its bell tower protrudes into the roadway, indicating the ancient nature of the building. The oldest part of the church, the square base, was built in 1678. It is surrounded on the north, south, and west by later additions, while the eastern wall remains untouched, preserving the altar apse, window frames, and old cornice. Originally, the church was likely single-domed.

The southern chapel in honor of the Beheading of St. John the Baptist was added in 1702 and combined with the refectory. In 1885-1886, it was enlarged by moving the apse eastward to align with the other altars. This chapel is now dedicated to All Saints who shone in the land of Russia.

In 1749, the church was rebuilt, acquiring its modern appearance. A new completion with arched niches and pilasters topped with an octagonal dome appeared over the old square base. At that time, the northern Nicholas chapel was added, consecrated in 1998 in honor of Seraphim of Sarov. The church acquired Baroque features, and it is possible that the reconstruction was carried out according to the project of a master from Prince D.V. Ukhtomsky's school.

In the Sergius Church, V.F. Odoevsky was baptized. In 1812, during the occupation of Moscow by Napoleon's army, the church was damaged and was assigned to the Church of St. John the Theologian. Services resumed in 1875.

On November 15, 1883, the church was handed over to the Patriarchate of Constantinople for the establishment of a metochion. In 1920, valuables were confiscated from the church, causing unrest among the parishioners. In 1934, the last Greek rector died, and the church was closed in 1938. In the late 1930s, a skate sharpening production was set up here. The church was consecrated on August 30, 1991, by Patriarch Alexy II and became a Patriarchal metochion.

In 2001, the bell tower was restored, and in 2010, the chapel in honor of All Saints was consecrated. In 2013, the painting of the Seraphim Chapel was opened. On the northern wall of the church, boards with inscriptions about buried parishioners are installed, among them representatives of the Ukhtomsky family. The necropolis of the Sergius Church is one of the most famous in Moscow.

Since 1991, the church has housed the Kievan Cross, a significant relic of Christianity made by order of Patriarch Nikon. The cross contains particles of the relics of 104 saints and 16 stones from Palestine. Among other relics of the church are the icons of the Mother of God Theodorovskaya and St. Sergius of Radonezh.