Reliable information about the monastery, which at that time was small and few in number, appeared in the mid-16th century. The late life of Cyprian of Ustyug states that the monastery existed in this place even in the pre-Mongol period. It is known that the monastery is located on Gledan Hill, where in the Middle Ages there was a Russian city called Gleden, founded, according to local legend, by Vsevolod the Great Nest.

With the increase in trade operations of Ustyug merchants in the 17th century, the Gleden monastery was strengthened. In the mid-17th century, thanks to the funds of the merchants Grudtsyn and with the blessing of Metropolitan Ion Sysoevich, the construction of brick buildings began. In 1697, the archimandrite administration was established at the Trinity-Gleden Monastery. At that time, the foundation of the monastery was associated with the year 1492, claiming that "the Trinity Gleden Monastery, it is said, was helped to build by the archangels, supplied with bread, and sent workers for the preparation and transportation of church timber."

The modern ensemble of the monastery was formed in the late 17th and the first half of the 18th century. First, a two-pillar Trinity Cathedral was erected, modeled after the cathedral of the Archangel Monastery in Ustyug. Then, the warm Tikhvin Church with a refectory, the Church of the Assumption of the Mother of God, and a hospital ward were built. In the 18th century, the Tikhvin Church was connected to the Trinity Cathedral by a covered gallery. The stone fence was never completed due to lack of funds.

In 1784, the creation of a new iconostasis in the baroque style was completed, which local masters worked on for eight years. The iconostasis of the old cathedral of the Yakovlevsky Monastery in Rostov was used as a model. This iconostasis has survived and is known for its wood carving.

The monastery was abolished in 1841 due to the small number of brethren and was annexed to the Mikhailo-Arkhangelsky Monastery. In 1912, it reopened as a women's monastery.

In 1925, the monastery was abolished again. The Trinity Cathedral with the iconostasis was assigned to the museum as an architectural monument, while the other buildings were used for a colony for orphans, a children's isolation home, a transit point for the dispossessed, a home for the disabled, and a nursing home.

In the early 1980s, the buildings were transferred to the museum.

On July 16, 2014, Bishop Ignatius Deputatov ordered the creation of the archbishop's courtyard "Trinity-Gleden Monastery."