According to the decree of Empress Catherine II from 1771, burials at parish churches within the city limits were prohibited, and it was mandated to create cemeteries outside the city. In 1775, the Peter and Paul Cemetery was opened with a stone church that has survived to this day. In 1891, a stone fence with two chapels was erected according to the design of architect Fyodor Vasilyevich Rybin. They were dedicated to St. Nicholas in honor of the salvation of the heir to the throne, Nicholas Alexandrovich, in Japan, and to St. Sergius.

According to the book by Archpriest Oleg Penazhko "Temples and Monasteries of the City of Kolomna", in the late 1960s and early 1970s, the cemetery was finally liquidated. The site, where many notable residents of Kolomna were laid to rest, including relatives of St. Filaret Drozdov, was leveled. In the 1970s, several architectural monuments of the cemetery complex were demolished, including a two-story clergy house and an almshouse from the 18th century, as well as one of the three chapels of the fence.

The Orthodox community of the Church of Peter and Paul was registered in 1997. In 2003, the community was given two surviving chapels dedicated to St. Nicholas of Myra the Wonderworker and St. Sergius of Radonezh, where regular services and memorials began to be held.