The monastery in honor of Saint Nicholas the Wonderworker was founded in 1573 by hieromonk Matfei, a Don Cossack, in a dense forest, which gave it the name Nikolo-Cherneev. In ancient documents, it was also referred to as "Matfei's Desert." The monastery was called Cossack because its construction was actively supported by the Don Cossacks. In 1663, ataman Osip Petrov wrote that the Cossacks had long been building the Cherneev monastery and made significant contributions. By the end of the 17th century, the monastery owned more than 600 peasant households, arable lands, forests, hayfields, and fishing grounds. It became wealthy mainly due to the contributions of the Cossacks, who, upon returning from campaigns, requested permission to go on pilgrimage to the monastery.

Initially, the monastery interacted with the Moscow state through the Cherkassy Cossack circle, but from 1686, it came under the jurisdiction of the Tambov diocese. The Cossacks were forbidden to interfere in the affairs of the monastery and accept its inhabitants, but they were allowed to make contributions, visit the monastery, and, with proper behavior, be tonsured as monks.

The abbots of the monastery have long held the title of archimandrites. In 1725 and 1764, the Vyshensky Assumption Monastery was annexed to the monastery. In 1764, the monastery was removed from the state list, but in May 1818, it became state-listed again. It was classified in the 3rd class and had up to 30 monks.

From 1912, the monastery became a female monastery, headed by abbess Margarita, with the number of sisters reaching 40. In 1926, the monastery was closed, and the presence of the sisters was prohibited, although the church continued to operate until 1936.

After its closure, the church was transferred to a local state farm: a granary was placed in the cathedral, a mill in the annex, a store and warehouse in the Church of the Kazan Icon of the Mother of God, and a water tank was installed in the bell tower. Workers lived in the brotherly buildings, and one of the buildings housed the management of the state farm.

In 1970, the monastery was transferred to the Zhelannovsky Local History Museum, and its director Nikolai Illarionovich Panin began the restoration of the buildings. In 1991, the monastery was returned to the Russian Orthodox Church for the revival of monastic life. The first abbot was igumen Feodosiy Agapov, followed by igumen Pimen Bakhanov, and from September 1998, Theofan Danchenkov, and since December 14, 2018, archimandrite Feodosiy Ivanov.