The history of the monastery goes back to a distant past. Some researchers believe that the monastery, originally called the Volyn Desert, emerged at the turn of the 14th-15th centuries, however, the first written mention of it dates back to 1505, which is considered the year of its foundation. In 1615, the monastery was burned by Polish-Lithuanian troops of False Dmitry, and only in the early 18th century were new stone structures built on the site of the wooden churches: the two-story Nicholas Church (the lower one consecrated in honor of the icon of the Mother of God "Sign of Kursk Root"), the Exaltation of the Cross Church, and the Trinity Church.

The modern appearance of the monastery is associated with the Rylsk merchants Shelikhovs, who generously donated to its needs. G.I. Shelikhov, known as the organizer of "Russian America," set off in 1783 on three galleots ("Three Hierarchs," "Simeon and Anna," "St. Michael") on a journey to the American shores. In addition to founding settlements and organizing economic life, he paid attention to the spread of Christianity, the construction of churches, and support for the Orthodox mission. Catherine II awarded him a silver sword and a gold medal with her portrait.

The miraculous appearance of the image of Saint Nicholas on the island of the Seym River near the village of Asmolovo in 1462 became a testament to the election of this place. A procession was held annually until 1917 in honor of this shrine, coinciding with the coronation of Nicholas Alexandrovich. During the Great Patriotic War, the monastery avoided destruction. Although the monastery was occupied by the Germans and shelled by our troops, not a single bomb fell on its territory. The Germans left the buildings intact when they abandoned the monastery.

In the 1920s, the monastery served as the residence of Rylsk Bishop Paul (Kroshchikin), who, after the death of Patriarch Tikhon, organized a secret collection of signatures for the election of a new Patriarch. The authorities brutally dealt with the participants of this action. Bishop Paul, who went through hard labor in the GULAG and arrests, was canonized in 2000. In 1926, the monastery was closed, its premises were used by Red Army soldiers and various secular institutions, leading to its destruction and desolation. In 1991, the Saint Nicholas Monastery was returned to the Kursk Diocese of the Russian Orthodox Church.