The Vazheozersky monastery was founded by the disciples of St. Alexander of Svir, the venerables Gennady and Nikifor. Elder Gennady first settled on the shores of Lake Vazhe around 1500 in a small cave. His food was herbs, and his bed was the earth. For his feats, he received great gifts from God, miracles, and healings even during his lifetime. Venerable Gennady passed away around 1516, having not established a monastery but sanctifying this place with his deeds and preparing it for the arrival of another disciple of St. Alexander of Svir, Venerable Nikifor.

In 1520, Venerable Nikifor, along with the inhabitants of the Svir Monastery, built a wooden Transfiguration church and several cells on the shores of Lake Vazhe, thus creating the Vazheozersky Spaso-Preobrazhensky Monastery. Venerable Nikifor became its first abbot and remained so until his death on February 9, 1557.

By a charter from Tsar Ivan Vasilyevich the Terrible, the monastery received lands "in all four directions for a verst, except for mosses, swamps, and boulders." The monks were to cultivate the land themselves, without hiring laborers or owning villages and peasants.

After the death of Venerable Nikifor, the abbot became Abbot Dorofey, who erected a chapel over the graves of the founders. In the early 17th century, during the Time of Troubles, the monastery was plundered by the Swedes, who destroyed property and killed part of the brotherhood, including Abbot Dorofey. The graves of the martyrs became a place of pilgrimage, but the monastery could not recover for a long time.

In 1640, Abbot Anthony became the head, who donated a valuable Gospel to the monastery and built a cell. However, the condition of the monastery remained poor. In 1680, Elder Savvaty became the builder, and by this time the monastery's property had significantly improved, and the number of monks and workers increased to 22.

In 1701 and 1764, the government of the Russian Empire conducted the secularization of church property, and the Nikifor Monastery was annexed to the Syandem Monastery, and then closed and converted into a parish church. In 1800, the monastery was again annexed to the Alexander-Svir Monastery.

In 1846, the monastery regained independence thanks to the efforts of Elder Isaiah. However, in 1885, the monastery suffered from a fire that destroyed all buildings except for a few. Restoration began thanks to the efforts of Abbot Veniamin and the support of St. John of Kronstadt.

After the 1917 revolution, monastic life was interrupted, and a monastic commune was organized on its lands, followed by a state farm and a children's colony. In 1922 and 1923, the monks were shot, and the monastery was destroyed. The revival of the monastery began in 1991 when it was returned its legal status. The monastery was revived as a women's monastery and then transformed into a men's monastery. In 2000, the relics of Blessed Monk Vladimir and parts of the relics of St. Prince Alexander Nevsky were transferred to the monastery.