The monastery housed a wooden Church of John the Baptist, residential buildings, a missionary school with a chapel, and utility structures. On the designated site, the patron of the fledgling monastery, Palladius, founded a wooden church in honor of the Nativity of the holy prophet John the Baptist.

All the monastery's buildings were destroyed in the early years of Soviet power. The authorities explained the demolition of the Bogodukhov Monastery as a necessity for constructing a thermal power station in a location with ample free space on Mount Mayak. The Church of John the Baptist, five residential houses for the inhabitants, a barn, an icehouse, a kitchen, a carriage house, and a shed, as well as two wings built in 1911, a kitchen with a shed and cellar, were all destroyed. An extension was added to the two-story building of the missionary station, where the office of the trust was located.

Currently, the territory of the Orenburg Bogodukhov Monastery is home to OJSC 'Orenburg Thermal Power Company.' The building of the former missionary station and part of the monastery fence have survived. All structures related to the Archierial House have also been demolished. The Nikolskaya Church, formerly Mitrofanievskaya, has been destroyed. The main building, the Archierial House, now houses City Hospital No. 2. The appearance of the building, once distinguished by magnificent architecture, has still been altered.