Before the monastery was founded, there was an Orthodox Nyatina Desert on the island. The monastery was established in 1520 by the Karelian saint Jonah, the son of the Novgorod mayor Ivan Klimentyev. Under Jonah, wooden churches of Nicholas and Trinity were built, but he did not become the abbot and remained a simple monk. Jonah passed away in 1534 and was buried near the walls of St. Nicholas Church.

In 1613 and 1614, the monastery suffered from Swedish raids. Until 1664, the superiors were abbots, and then builders. In 1709, the Nicholas Church burned down, and in 1712, the Trinity Church was rebuilt. In 1714, the Meeting Church was erected, which was reconstructed and consecrated in the name of St. Nicholas the Wonderworker in 1843. A stone church in the name of the Righteous Zacharias and Elizabeth was built with funds from Empress Elizabeth, which was re-consecrated after repairs in 1840. This church housed the tomb of Jonah of Klimenets.

Since 1764, the monastery became a non-staff one, and in 1769 it was abolished. From March 1772, the churches of the monastery came under the jurisdiction of the Sennogubsky parish. In 1833, the monastery was restored by the first Bishop of Olonets and Petrozavodsk Ignatius, who transferred it under the authority of the manager of the Olonets episcopal house, Jonah. Ignatius donated part of his property to the monastery and wrote an essay on its history.

In 1853, restoration works on the monastery buildings were carried out under the project and supervision of the Olonets provincial architect V. V. Tukhtarov. On April 23, 1860, the monastery gained independence. In 1876, a rescue station was opened at the monastery, headed by the abbot. In 1884, Grand Duke Vladimir Alexandrovich visited the monastery. It became a pilgrimage site for worshippers from Petrozavodsk.

In 1901, at the initiative of the archimandrite Varna, a literacy school was opened, which was transformed into a church-parish school in 1902. In 1903, it was sponsored by Grand Duke Konstantin Konstantinovich. On April 5, 1902, the monastery suffered from a fire. In 1905, a wooden church in the name of St. Jonah of Klimenets was consecrated. In 1906, the monastery became a female monastery. During World War I, the nuns collaborated with the All-Russian Union for Assistance to Sick and Wounded Soldiers.

The insurance inventory of 1913 included 27 buildings on the monastery grounds, the church of Zacharias and Elizabeth, a bell tower, the church of Jonah of Klimenets, a quadrangular chapel, a tower, cells in the southeast corner of the fence, a new two-story brotherly building on a stone foundation, a two-story small brotherly building, a wooden refectory, a house, a cell, a cellar, a pit, and an icehouse.

In 1920, the monastery buildings were transferred to a local state farm and were later used for workshops for a home for the disabled and a pioneer camp. In 2015, a parish of the church of the Righteous Zacharias and Elizabeth of Klimenets Monastery was established. The abbot became Hieromonk Alexander Marchenko, who was the prior of the Kem Blagoveshchensky Men's Monastery from 2000 to 2015. In May 2016, the first monks returned to the reviving Klimenets Monastery, and construction and restoration work began. For the organization of the monastery's courtyard, a house where Metropolitan Manuel Pavlov lived was transferred by Metropolitan Konstantin of Petrozavodsk and Karelia.

On September 3, 2017, Metropolitan Konstantin consecrated the church built on the old foundation in the name of St. Nicholas the Wonderworker.