The history of the Vyshensky Uspensky Monastery is known both from legends and from documents presented in the book by Igumen Tikhon Tsiplyakovsky, published in Tambov in 1881. It is believed that the monastery was founded in the 16th or 17th centuries, and it is first mentioned in written sources in 1625 in a charter from the mother of Tsar Mikhail Fyodorovich, Marfa. This charter speaks of the relocation of the Church of the Assumption of the Blessed Virgin Mary and the construction of the monastery at a new site, although the community already existed on the left bank of the Vysha River. Marfa Ioannovna allocated a new site for the monastery near the navigable Tsna River. The old site, known as 'Old Desert and Garden', remained the property of the monastery until 1897, when a land exchange occurred with landowner Emmanuil Dmitrievich Naryshkin. Since 1625, the construction of the desert was overseen by Hieromonk Tikhon, and later by Igumen Gerasim, who expanded the land holdings of the community. In 1724, due to a lack of brethren and poverty, the monastery was abolished and attached to the Cherneevsky Nikolsky Monastery, with only four residents remaining. However, it was soon restored, and by 1737, the monastery had two wooden churches and three cells, but no income. In 1740, Hieromonk Philaret became the abbot, followed by Hieromonk Avraamiy in 1753. Under Igumen Dosifei, the construction of a stone church began, consecrated in 1762. In 1764, the monastery became independent. In 1774, the cathedral Assumption Church was robbed, but the monks were not harmed. In the 1780s, Hieromonk Leontiy was the abbot, during whose tenure land surveying was conducted and property inventories were compiled. He was succeeded by Hieromonk Ioann, and then by Hieromonk Lavrentiy, under whom a chapel in honor of St. Sergius of Radonezh was arranged in the church.

A new stage in the history of the monastery began in the 19th century when it came under the jurisdiction of the Tambov Diocese under the administration of Archbishop Theophilus. Thanks to him, Hieromonk Tikhon was transferred from the Sarov Monastery, who practically rebuilt the Vyshensky Monastery from scratch. Under him, a stone bell tower, cells, and a fence were erected. The main shrine of the monastery became the Kazan Icon of the Mother of God, transferred to the community in 1827. In 1866 and 1894, Bishop Theophan lived in the monastery, leading a secluded life. In 1862, he appointed Arkadiy as the igumen, under whom many new buildings were constructed, including the brotherhood building and guesthouses. A procession with the miraculous icon was also established.

In the 1920s, the monastery was closed, its buildings and property nationalized, and the monks evicted. The book 'Red Terror in Russia' describes how peasants in the Shatsky district of the Tambov province tried to protect the Vyshinskaya Icon of the Mother of God from desecration but were shot. The only place where services continued was the Christ-Birth Cathedral. The territory of the monastery was used for various needs, including a psychiatric hospital. In 1972, a group of clergymen secretly transported the relics of Bishop Theophan from the monastery. In 1988, Theophan the Recluse was canonized, drawing attention to the abandoned community. In 1990, the revival of the monastery began, and part of the buildings was transferred to the church to establish a women's monastery. In 2002, the solemn transfer of the relics of Saint Theophan to the Vyshensky Monastery took place.