Information about the time of the monastery's foundation varies: some sources claim it was founded in 1605, others in 1622. However, it is known for certain that the monastery existed in the 1630s. A. Latyshev explains its early appearance in the newly founded city by government decrees. The original population of Tomsk consisted of unruly Cossacks, greedy industrialists, foreign fortune seekers, exiled Poles, deported convicts, and local Tatars. "The government saw the need for such a place to establish an example of Christian virtues..."

In the 1630s-1650s, the Bogoroditsky Monastery was located at the confluence of the Kirgizka River into the Tom River (Ust-Kirgizsky Monastery). In 1658, it was moved to Yurt Mountain, where underground storages and passages to the Ushayka River were created during construction. In 1663, the church was consecrated in honor of St. Alexey, the man of God, and the monastery became known as the Mother of God-Alexey Monastery.

From this monastery, the leadership of eight Siberian monasteries, which were part of the Tomsk rank, was carried out. Until 1764, it was the only owner of 400 serfs in the Tomsk province and possessed land on the Tom and Ob rivers. In the 17th century, a hospital was opened at the monastery, and in 1746, the first Tomsk school. Since 1858, a theological seminary with an extensive library operated here.

The monastery, like other Siberian monasteries, served as a place of exile for violators of monastic rules, as well as for the detention of secular individuals.

The main church of the monastery is the Kazan Church with chapels in honor of Alexey, the man of God, and saints Flora and Lavra. Originally wooden, it burned down several times. In 1789, a modern stone building in the style of Siberian Baroque was constructed, which housed the especially revered icon of the Mother of God "Burning Bush."

In 1922, the monastery was closed, and the monks and archimandrite were executed on Mount Kashtak. The buildings of the monastery were repurposed for the Industrial-Pedagogical Institute.

In 1992, the Kazan Church and the monastic cell building were returned to the faithful.

In 2012, 15 million rubles were allocated from the federal budget for the restoration of the Kazan Church under the program "Culture of Russia."