The history of the monastery begins in 1883. The owner of the estate in the village of Bykovo, Yelisaveta Yermolinskaya, submitted a written request to Archbishop Ionafan of Yaroslavl and Rostov to establish a women's community on her estate covering 175 desyatins. On December 25, 1885, the Holy Synod approved the creation of the Pokrovskaya community. In 1892, it was transformed into the Mologsky Pokrovsky Women's Monastery.

On March 18, 1886, the Yaroslavl Spiritual Consistory appointed nun Serafima Fyodorova from the Yaroslavl Kazan Women's Monastery to the new monastery. In 1893, there were 93 residents in the monastery, and by 1927, when the monastery was closed, their number had reached 200. In 1895, a dependency with a stone chapel was established in Rybinsk, which was confiscated along with its property in 1919.

After the monastery was closed in 1927, an agricultural school and workshops were set up on its territory, and a club was arranged in the Church of St. Sergius of Radonezh. The altar of the Church of the Protection of the Holy Virgin was completely demolished, and a tractor workshop was placed there. The monastery cemetery was turned into a stadium.

In 1940, after the construction of the Rybinsk Hydroelectric Power Station and reservoir, the city of Mologa was flooded along with its churches and monasteries, including the famous Leushinsky Monastery. Residents of the flooded areas were relocated, but the Pokrovsky Women's Monastery remained unflooded. In 1996, the monastery was transferred to the Yaroslavl Diocese.

There are two churches on the monastery grounds. The stone church in honor of the Protection of the Holy Virgin with a single altar was built in 1889 and is currently in a semi-ruined state. The domestic church in honor of St. Sergius of Radonezh is located inside a three-story stone building, where the heating system has failed, making worship impossible.