The monastery was founded in 1640 at the Yakut ostrog by Igumen Nafanail from Vologda with funds donated by Tsar Mikhail Fyodorovich. The first church of the monastery was consecrated in honor of St. Michael Malein.

Due to frequent relocations of the ostrog, the location of the monastery was unstable. In 1663, the servicemen of the Yakut ostrog decided to establish a monastery in the name of the Savior and appointed Ivan Afanasevich Ovchinnikov as the priest and builder of the monastery. In 1663 and 1665, the monastery received donations from Tsar Alexei Mikhailovich, with which the Spasskaya church was built.

The small brotherhood of the Spassky monastery, in addition to conducting services, engaged in spreading the foundations of the Orthodox faith and literacy among the local population.

In 1735, Archimandrite Nafanail, by the order of Bishop Innokentiy Nerunovich of Irkutsk, organized the first school in Yakutia for the education of local children at the monastery, but it closed in 1747.

In 1764, during the reforms of Catherine II, the monastery was removed from the synodal jurisdiction and was maintained only by donations. In 1766 and 1769, it was necessary to liquidate the monastery's economy and sell livestock.

In 1800, by the decree of Emperor Paul I, a school was opened at the monastery, which became the Yakut Spiritual School in 1818 for training church personnel.

From the 19th century, the monastery was again allocated state support and land; it was first classified as 3rd class, then as 2nd class. The construction of the stone Spasskaya church began. In 1820, the old Nikolayevskaya church was moved to the territory of the monastery from the city market.

In 1853 and 1860, the first archbishop with a residence in Yakutsk, Saint Innokentiy Veniaminov, was at the monastery, who was the abbot. Under him, construction unfolded: in 1859, the archbishop's house with a cross church was built. In 1866, a new stone temple in honor of the Uncreated Image of the Savior was consecrated. The monastery was located on the deserted outskirts of the city.

In 1870, with the establishment of the Yakut Diocese, the monastery came under the jurisdiction of the diocesan archbishop, and the abbot was given the title of vicar and the rank of igumen.

In 1884, a missionary school and a spiritual seminary were opened at the monastery, and in 1888, a women's diocesan school.

In April 1904, the monastery was merged with the archbishop's house. At the beginning of the 20th century, there were 4 inhabitants in the monastery, and it owned 8,020 desyatinas of land. Almost all the property was rented out.

In March 1919, the Yakut Revolutionary Committee closed all spiritual institutions. In 1920, by the order of the White Guards, property and food were confiscated from the monastery, leaving the monks with the minimum for survival. After the restoration of Soviet power, the monks sought help but were refused.

By 1921, the monastery ceased to exist as an economic entity. The Revolutionary Committee found only 30 barrels of cement on its territory. The monastery was nationalized, and the buildings were transferred to the Local History Museum.

Most wooden structures burned down. The stone cathedral and the cell building were dismantled. In 1923 and 1974, one of the former monastery buildings housed the Central State Archive of the Yakut ASSR, which was later demolished. Only the former archbishop's quarters remained, which became the building of the Yakut State Museum.

In August 2011, Bishop Roman Lukin of Yakutsk and Lena announced the restoration of the monastery. On August 19, the Spassky temple was laid at the historical site. A temple-wagon was brought to the territory, around which a community of believers gathered. The monastery is set to become a missionary center.

Construction materials were acquired, and on April 19, 2012, the first pile was consecrated. After the completion of the temple's construction, the restoration of the brotherhood building is planned.

The church was returned only part of the monastery's territory, the rest is occupied by the museum.

On October 2, 2013, the Holy Synod of the Russian Orthodox Church officially established the monastery, appointing Hieromonk Nikon Bachmanov as the igumen.

On October 6, 2013, Bishop Roman Lukin elevated Hieromonk Nikon Bachmanov to the rank of igumen.