The monastery was founded in the second half of the 16th century by the venerable Iona of Yashezero, a Vepsian by nationality, near his native village of Shoksha, on the shores of Lake Yashezero. This place previously served as a pagan shrine, symbolizing the victory of Orthodoxy over paganism.

The first mention of the monastery dates back to 1562 and is found in a donation book created to raise funds for the monastic community. This year is considered the date of the monastery's founding. At that time, a wooden church was built in honor of the Annunciation of the Most Holy Theotokos, as well as monastic cells and economic buildings.

On June 1, 1589, at the request of Iona, Elder Joseph, and the brotherhood, the Metropolitan of Novgorod and Veliky Luki, Alexander, signed a decree freeing the monastery from taxes. With the collected funds, the Church of the Transfiguration of the Lord was built in 1629.

In 1725, the monastery was attached to the Klimentetsky Men's Monastery. On May 14, 1726, by the order of Archimandrite Kirill, the Yashezer Desert was subordinated to monk Niphont. In 1734, it was fully transferred under the administration of the Alexander-Svirsky Monastery.

On April 3, 1741, Hieromonk Cornelius entrusted monk Gennady with the supervision of the churches and church utensils in the Yashezer Monastery. However, Gennady arrived there only in 1744, and by that time the monastery was in decline, with no more than five heads of livestock.

According to Catherine II's reform of 1764, the monastery was abolished and attached to the Novgorod Archiepiscopal House, to the Ivin parish of the Petrozavodsk district.

With the funds of Petrozavodsk merchant Mark Pimenov, the Church of the Transfiguration of the Lord was built. From 1852 to 1857, the monastery was attached to the Olonets Archiepiscopal House. In 1853, under the guidance of architect V. V. Tukhtarov, restoration work was carried out on the monastery buildings.

On September 12, 1857, by decree of the Holy Synod, the Yashezer Desert gained independence due to improvements in its situation through donations and income, which allowed for the construction of a fence with towers, cell buildings, a guesthouse, and economic structures.

In 1903, there were eight monks living in the monastery, and by 1907 their number had increased to 12. In 1918, the last seven monks, who refused to leave the monastery, were shot, the monastery was closed, and its property was nationalized. Various institutions were placed on its territory, and by the 1980s most of the buildings were destroyed.

In the 1990s, the ancient wooden church of the Annunciation of the Most Holy Theotokos was burned down. Only the dilapidated Church of the Transfiguration of the Lord, the corner towers of the stone fence, and two small buildings remain.

In 2003, the Holy Synod decided to revive monastic life in the Blessed Annunciation Iona-Yashezer Monastery. Thanks to the efforts of Igumen Dosifei, a Board of Trustees for its salvation was established in 2004.

The revived monastery needs complete restoration; the buildings are destroyed, and the brotherhood does not reside there. Currently, there are four people in the monastic brotherhood, who live at the dependency in the village of Sholtzero, established in 2004.

A passportization of the monastery buildings has been conducted, and the construction of a new Church of the Annunciation of the Most Holy Theotokos is being planned. However, the lack of a road to the monastery complicates restoration work. In 2012, thanks to the owner of a nearby tourist base, part of the potholes on the road was filled with gravel. The lack of funds and patrons threatens the preservation of the monastery complex.