The two-storey Isidore Church, where the Estonian parish had held its services until the 1930s, is near Mogilevsky Bridge. The construction of a church for the Estonian Orthodox brotherhood was suggested by the rector of the parish, Pavel Kulbush. The project of the temple was presented in 1901 by architect Aleksandr Artemyevich Polishchuk, who was also a member of the society of the Holy Hieromartyr Isidore of Yuriev. According to the architect's plan, the stone five-domed church was to be pillar-free.

The first donation for the creation of the temple was made by St. John of Kronstadt. Emperor Nicholas II also made his contribution. Thanks to the funds of philanthropist Ivan Bogdanov and other patrons, the construction was completed in 1907.

In Soviet times, the redeveloped building housed the workshops of the painting and decoration factory of the USSR Art Fund.

Since 1999, both the upper and lower temples have been restored. The Baroque iconostasis of the Isidore Sacrarium was restored with the use of pre-revolutionary models. Now the green-headed church is a single ensemble with an adjacent residential building.