The church in question is the only remaining reminder of the settlement of migrants from Veliky Novgorod in Lubyanka. These people were relocated to Moscow not of their own will, but by the order of the Grand Duke of Moscow, and they sought to create something in their new place that resembled their hometown.

Until 1922, Pushkin Street was called Sofiyskaya in honor of the Church of the Wisdom of God. This name was chosen not by chance: after the annexation of the Novgorod Republic to the Moscow principality, many noble Novgorodians were relocated to the capital, and their places were taken by people loyal to the new authorities. The settlers established a compact settlement and named the neighboring street after the Lubyanka district, and they built a church reminiscent of the St. Sophia Cathedral. The first wooden church of St. Sophia is mentioned in 1480. The Novgorod style of the church emphasized the chapel in honor of St. Nikita of Novgorod. The church building was renovated several times: in 1650 it was rebuilt, and in 1685 it burned down. With the funds of the nobleman Moses Ovtsyn, the construction of a stone church with a chapel of St. Nicholas the Wonderworker began in 1691 and was completed a year later.

The main part of the church has been preserved since the late 17th century, but over time it was built up with new elements of the refectory and bell tower, and the original facade was altered. Instead of five domes, a single dome appeared in the second half of the 18th century, the windows were enlarged, and the frames were lost. The bell tower was built in 1816 in the Empire style, with Tuscan porticos and rusticated treatment, and the ringing tier was made octagonal with a spire. The refectory was rebuilt in 1842, and at that time a second chapel in honor of the Kazan Icon of the Mother of God was added. Due to the corner location to Pushkin Street, the structure of the building turned out to be asymmetrical, and the Kazan chapel was made truncated to comply with the red line of the street.

By 1932, the church was closed and handed over to the state security agencies. The church lost its dome and the top of the bell tower, the porticos were destroyed, and it became the Experimental Factory of Sports Products of the Dynamo Society. By the 1980s, the historical surroundings of the church were completely demolished, but the building itself was preserved. The territory of the churchyard was built up with new buildings of the state security. Since 2001, services in the church have resumed, and it has received the status of a parish church under the FSB.