The idea of building a stone church over the Caves in honor of the Chernihiv icon of the Holy Mother of God belonged to the abbot Daniil and was realized according to the project of architect Nikolai Vladimirovich Sultanov. This endeavor involved abbot Daniil, the treasurer of the Trinity-Sergius Lavra, archimandrite Afanasy, the assistant economist of the lavra, hieromonk Gennady, the head of the cave monastery, hieromonk Nektary, as well as numerous brethren of the skete and caves. The church was envisioned to be spacious and built in the style of Russian architecture of the second half of the 17th century.

The Gethsemane skete did not have the means to construct such a luxurious church, so it had to seek help from benefactors. The request was answered by honorary citizen Sergey Pavlovich Patrikeev, merchant Mikhail Vasilyevich Morgunov, princess Elena Petrovna Cherkasskaya, peasant from Vladimir province Daniil Vasilyevich Kiselev, and many others.

On September 28, 1886, the solemn laying of the future church took place, conducted by Metropolitan of Moscow Innocent Rudnev.

The church was soon built. It was adorned with two chapels: in honor of the holy righteous princes Boris and Gleb, constructed with the funds of Princess Cherkasskaya and consecrated in 1889 by Metropolitan Ioannikiy, and in honor of the Prophet of God Elijah, built thanks to the contributions of merchant I.V. Patrikeev and consecrated in 1890. Princess Cherkasskaya also arranged a cave church in the name of Anthony and Theodosius of the Kiev Caves, where she was later buried.

On August 26, 1893, during the feast of the Vladimir icon of the Mother of God, the main chapel of the church in honor of the Chernihiv icon of the Holy Mother of God was consecrated. The consecration was performed by Bishop Dmitrovsky Alexander Svetlakov, who managed the Moscow diocese.

The church turned out to be very beautiful both outside and inside. It was spacious and bright, with a luxurious metal iconostasis made with the funds of merchant A.I. Osipova. Inside, there was exquisite wall painting in the style of the 16th century, created by icon painter N.M. Safonov, and the floor was laid with mosaic patterns. In terms of the richness of decorations and artistic level, the Chernihiv church was considered one of the most famous in Russia.