The Our Lady and St. Alexey Monastery was founded in 1605, the following year after the foundation of Tomsk. It is on Yurtochnaya hill over the river Kirgizka. The main halidom of the monastery is the relics of St. Feodor of Tomsk, better known as Feodor Kuzmich. They are kept in a chapel on the territory of the monastery.

There is a legend that claims that the Russian emperor Alexander I faked his death in Taganrog in 1825 to become a hermit. Feodor Kuzmich, who was sainted by the Russian Orthodox Church, was a real person. However, historians still uncertain whether he was the former Russian emperor.

The first records of Feodor Kuzmich date back to 1836 when he was arrested for vagrancy in Perm. Feodor Kuzmich had no identity papers on him and after whipping he was exiled to Siberia. He settled in the Beloyarskaya stanitsa near Tomsk. During the lifetime of Feodor Kuzmich in Siberia there were strong rumours about his being the former emperor, but he led a very secluded existence and died in 1864. Feodor Kuzmich was buried at the Monastery of the Virgin and Saint Alexey.

At first, the Church of St. Alexey was the main temple of the monastery. The monastery itself was also named after this saint. But in 1776 the church was burnt from a stroke of lightning. A new stone church was laid down, which was consecrated in honor of the Icon of Our Lady of Kazan. In 1830 the monastery was surrounded by strong walls and was sometimes used as a place for exile.