As built, the church was richly decorated with a three-tiered iconostasis and paintings and sculpture from some of Russia's leading artists.

In 1881 the Dukhovskoy Church hosted the funeral of author Fyodor Dostoevsky, and in the mid-1890s a small chapel was consecrated to Saint Evdokia.

Despite calls to protect the important historical and artistic heritage of the church, it was not one of those selected for conversion into a museum necropolis during the Soviet period and was instead passed through various organisations, who at times used it as a boiler room, for coal storage, or as temporary accommodation.

It was once again confiscated by the city authorities during a period of anti-religious campaigning and hosted a blood transfusion station until its return to the monastery in the early 2000s.

The Dukhovsky wing of the monastery, linking the Holy Trinity Cathedral and the Annunciation Church, was designed by Domenico Trezzini in the Petrine Baroque style.

[2][3] On 23 May 1820 construction started on a house church for the wing, by order of Metropolitan Mikhail [ru], and to the design of architect Vasiliy Petrov.

[4] The altarpiece, titled "Transformation" was painted by A. V. Shevelykin, while further decoration was provided with a series of evangelical images by M. K. Nabokov and stucco works by N.

[2][5] Between 1894 and 1895 a small chapel with a single-tier iconostasis was built to the right of the altar, over the crypt of the Galunov family, and consecrated on 12 March 1895 by Metropolitan Palladiy to Saint Evdokia.

[1][2] A commission, consisting of representatives from the Institute of History, the Communist Academy, Pushkin House, the Academy of Material Culture, the Committee for the Preservation of Monuments, the Museum of the City, and others, proposed that the Dukhovskaya Church be protected in the same way as the Annunciation Church, "because of the presence of a large number of museum valuables and historical burials".

[3] The proposal was ignored, and in July 1936 the city administration turned the Dukhovskaya Church over to the "Lengorplodovoch" organisation, which demolished many of the funerary monuments to install a boiler room and coal storage.