The monastery of St. Philipp Irapsky was founded in 1517 during the reign of Grand Duke Vasily Ivanovich. During the Time of Troubles, from 1611 to 1618, the monastery was attacked by Polish-Lithuanian invaders and was burned and destroyed, with only the churches remaining. In 1676, the monastery was restored, and in 1688 it was assigned to the Patriarch of the Resurrection Monastery in Cherepovets. In 1699, a stone monastery was built on the site of the desert, which lasted until the 1920s. In 1764, with the establishment of monastic states, the Trinity Philipp-Irapsky Monastery was abolished along with the Cherepovets Resurrection Monastery, the monks were distributed to monasteries in Vologda, and a parish priest was appointed to the desert. The monastery remained abolished for 28 years.

In 1914, the abbot of the desert became Hieromonk Leonid Molchanov, who actively worked on its material and ecclesiastical strengthening. In March of the following year, he was elevated to the rank of igumen. In 2005, his name was included in the Assembly of New Martyrs and Confessors of Russia of the 20th century. In 1918, while being the abbot of the Solvychegodsk Vvedensky Monastery, Leonid was recognized as an enemy of the Soviet government and was shot. In the same year, the monastery's property was nationalized, a children's home for orphans of the civil war was opened, and the monks were forced to work in an agricultural artel. From 1925, a rest house "Andoga" was located in the desert, and in 1927 the monastery was closed. The bell from the bell tower fell into the Andoga River and still lies at the bottom opposite the monastery gates. During the Great Patriotic War, a hospital was placed in the monastery, which after the war became a home for the disabled, and since 1974, a boarding school for the mentally ill.

The restoration of the monastery began in the summer of 2016, when most of the buildings were in emergency condition. In August, an archbishop's courtyard was opened under the leadership of the abbot Hieromonk Theodosius Belov and builder Hieromonk Geronty Chudnevich. In six months, the cell buildings, refectory, bathhouse, and hotel were restored, roofs were renewed, the restoration of the Kazan Church of 1755 is underway, and a new wooden chapel has been built. The area around the monastery has been cleared, and the number of residents has increased to 30 people.

Plans include the complete restoration of all monastic buildings, including three churches: Kazan, Trinity Cathedral, and the chapel of Philipp Irapsky, strengthening the banks of the Andoga, creating bathing facilities, laying out a monastery garden, and setting up livestock yards. It is expected that the monastery will provide itself with bread, milk, and prosphora.

Since August 2016, regular services have been held in the domestic church of the monastery. On November 27, 2016, and April 22, 2017, Liturgies were held for the first time in 90 years in the restoring Kazan Church, and on April 22, 2017, the first procession took place. On May 21, the first archpastoral Liturgy in 100 years was held in the monastery, gathering a record number of pilgrims. Thus, the monastery is being revived both externally and spiritually.