The monastery was founded on August 19, 1260, when the Belozersk prince Gleb Vasilkovich, grandson of the Grand Prince of Rostov Konstantin Vsevolodovich, was saved from a storm and vowed to build a monastery at the place where his ships would land. The waves brought the ships to Kamen Island on the day of the Transfiguration of the Lord, where the prince found hermits preaching Christianity among the local pagans. They had a chapel for prayers. The prince fulfilled his vow by building a church in honor of the Transfiguration of the Lord and establishing the monastery, with Elder Feodor as its abbot.

From the very beginning, the Spaso-Kamen Monastery was under the protection of the Belozersk princes and quickly prospered, attracting ascetics and strengthening its material position. Since the time of Prince Dmitry Donskoy, the monastery became known to the Moscow princes.

In the 15th century, the Spaso-Kamen Monastery became a significant religious and cultural center, where Dionysius Glushitsky, Alexander Kushtsky, and Joasaph Kamensky labored.

In 1925, the Soviet authorities closed the monastery. The monks were expelled, and attempts were made to turn the buildings into a colony for juvenile delinquents, who soon scattered. In the autumn, a fire damaged many structures. After the closure, the oldest church of the Russian North was destroyed by an explosion, leaving a pile of rubble.

In 1937, the Spaso-Transfiguration Cathedral was blown up for bricks to build a House of Culture, but it was never used. During the Great Patriotic War, a fish reception and processing point was organized on the island.

In 1991, architect Alexander Asafov and engineer Alexander Pligin began restoring the monastery with the blessing of Archbishop Mikhail Mudjugin. After Asafov's death and the cessation of funding, Pligin continued the work at his own expense, relying on the help of family and friends. They restored the monastery hotel, built a chapel, and began the restoration of the Assumption Bell Tower.

In 2006, the archbishop's courtyard "Spaso-Kamen Monastery" was established on the island, with Hieromonk Dionysius Vozdvizhensky as its abbot. In 2009, the first service was held in the Assumption Church, and in 2010, Archbishop Maximilian consecrated the church, making the services regular.

By 2010, the restoration of the Assumption Church-Bell Tower was completed. Since 2012, Hieromonk Nestor Kumysh became the abbot. In 2015, the reconstruction of the brotherly-abbot's building began, but funding was suspended in 2016 and 2017.

On October 6, 2017, the Holy Synod decided to open the Spaso-Kamen Transfiguration Men's Monastery and appointed Hieromonk Dionysius Vozdvizhensky. In 2018, a competition was announced for the restoration of the Church of the Assumption of the Most Holy Theotokos. The work was estimated at 31,969,659 rubles. That same year, the restoration of the brotherly building began.

On September 23, 2018, the relics of St. Joasaph Kamensky were returned to the monastery. On May 5, 2019, Metropolitan Ignatius Deputatov called for fundraising for the clearing of debris and the restoration of the main church of the monastery.