The church in honor of the holy princes Boris and Gleb is located in the ancient part of Kolomna, known as Zaprudy, where merchants and craftsmen once lived. The first mention of the church appears in documents from the 16th century. Until the 17th century, it was wooden. The church icon from the 14th century "Saints Boris and Gleb with their lives" is now kept in the State Tretyakov Gallery.

The stone church was built between 1716 and 1726 by an unknown architect in the style of Russian Baroque, funded by local residents K. Zhitnikov and N. Nabokov. In the second half of the 18th century and the beginning of the 19th century, the church was rebuilt: a refectory in honor of the righteous Zacharias and Elizabeth was added. The five domes on thin light drums were preserved, but the domes were placed at the corners. The window frames were simplified, and a porch with columns was added to the southern boundary. Not far from the church was the house where the writer I.I. Lazhechnikov was born, baptized in this church. It is likely that his family were parishioners of the church. It is known that in the early 20th century, the Borisoglebsky church was often visited by F.I. Shalyapin, who liked its acoustics. A church parish school operated at the church.

During the Soviet era, the church building was used as repair workshops and warehouses. During the Great Patriotic War, tanks were repaired here. The church suffered greatly: the bell tower was destroyed, the small domes were knocked off, the wall paintings were painted over, the church utensils were looted, and a wall was broken in the refectory for tank entry. The floor was damaged by a pit for repairing equipment. The church fell into disrepair, and no one monitored its condition. There were even attempts to make a second floor in the Borisoglebskaya chapel, and the rails for the ceilings have not yet been dismantled due to the complexity and high cost of the work.

In 1995, the church was returned to the believers, and restoration began. In 2007, the exterior finishing of the chapel was completed; it was plastered and painted red, symbolizing martyrdom. On the eve of the Day of Slavic Writing and Culture and before the church's feast day on May 13, 2007, gilded crosses were placed on the domes. In the Zacharias and Elizabeth chapel, thanks to benefactors Gleb and Ilya, a two-tiered carved iconostasis was installed. The altar received an altar table and a sacrificial table, as well as all the necessary utensils for worship. In the autumn of the same year, services began to be held in the Zacharias and Elizabeth chapel.