The Muyezersky Monastery was founded in the mid-16th century by monk Kassian Muyezersky from Solovki. Although the exact dates of his life and canonization are unknown, he is included in the Assembly of Novgorod Saints.

The monastery had a church in honor of the Life-Giving Trinity, which has not survived. In 1602, a warm wooden Nikolskaya church was built, shaped like an elongated square with a gabled roof on the porch and altar, single-domed with a spire.

There was also a bell tower and a cell chapel of the Savior Not Made by Hands, which housed wooden crosses: a four-meter one made by Elder Alexei in 1672, and a three-meter one. In the altar of the Nikolskaya church stood a cross with the inscription: "This cross was erected by the original elder monk Gennady in the year 1573 on August 11." In the early 1960s, this cross was taken to Leningrad by an expedition from the Russian Museum.

In 1580, the monastery, under the command of voivode Kypriyan Onichkov, withstood a siege by three thousand Swedes. By decree of Catherine II, in 1764, the monastery was abolished, and the churches were for a long time part of the Maslozersky parish and did not have their own clergy.

After the abolition in the 18th century, Old Believer monks settled in the monastery, and an Old Believer cemetery was preserved. To this day, the Nikolskaya church, restored in 1976, where a service is held once a year, and the chapel in honor of the Savior Not Made by Hands have survived.

A chapel-tomb with a coffin has been preserved, in which the relics of one of the builders of the monastery, presumably Kassian Muyezersky, may be located. According to other sources, the venerable Kassian died in the Spaso-Preobrazhensky Ken Monastery, and his relics were transferred to the Antoniev-Siy Monastery.

By a resolution of the Council of Ministers of the RSFSR, the Nikolskaya church and chapels have been recognized as architectural monuments and objects of cultural heritage of Russia. On December 12, 2014, a meeting took place at the Ministry of Culture of the Republic of Karelia between Bishop Ignaty of Kostomuksha and Kem and Minister of Culture E. V. Bogdanova, where issues regarding the revival of the Trinity Muyezersky Men's Monastery were discussed.