The stone church of the Transfiguration of the Lord was built with funds from Petrozavodsk merchant of the first guild and honorary citizen Mark Pimenov between 1853 and 1855. Its consecration took place on June 10, 1855. A total of 15 thousand silver rubles was spent on its construction. In 1856, a gilded carved reliquary was installed over the relics of the saint resting in the church by merchant Mark Pimenov and his wife Matryona Timofeevna. The upper board depicts the saint Jonah of Yashezero in a silver robe of 84 fineness with a gilded crown. The weight of the robe is 14 pounds and 44 zolotniks, and it is surrounded by an iron grille.

On September 12, 1857, by decree of the Holy Synod, the Yashezero Monastery gained independence with the establishment of a builder and the appointment of a staff of seven monks. Thanks to donations and income from the monastery lands, a new complex of buildings was constructed, predominantly made of stone. A new fence with towers at the corners and two two-story cell buildings were erected. Outside the fence, a guesthouse for pilgrims and utility buildings were constructed: a cattle yard, a hay barn, a stable, four barns, a forge, a bathhouse, a tar distillery, a rig, a carriage house, a laundry, and others. From this moment, the monastery experienced its second birth.

Hieromonk Nafanail, a direct witness to these events, noted in his report to Bishop Arkady: "The execution of the entire church construction according to the plan and facade is excellent. The church is not yet plastered on the outside, but it will be remarkably beautiful. This warm stone church, a great adornment of the Yashezero Monastery, is a true comfort and joy for the local residents, who regard the sanctity of this place with reverence due to the relics of the holy founder of the desert, the venerable Jonah." In September of the same year, icons for the three-tiered iconostasis of the Transfiguration Church, commissioned and funded by a benefactor from St. Petersburg, were delivered to the monastery. "I have seen these icons," Nafanail continues, "but not being knowledgeable in icon painting and painting, I do not dare to assess their artistic value. I will only say that such icons are a rarity in this region. During my time, writes Nafanail, as if for good fortune, a cow was brought as a gift to the monastery, and it was promised to bring two more from Ladva and Shoksha."

During the Soviet era, the monastery was abolished and closed, and its property was nationalized. The territory of the monastery housed penitentiary institutions, summer camps, forestry enterprises, and logging companies. Due to such use, the monastery quickly fell into decline and by the early 1980s was largely destroyed.