The beauty and significance of the Admiralty Church lie in its main square nave, created by Moscow architects. The five domes adorning the temple testify to the influence of the new style brought to Moscow by Ivan III. A characteristic feature of that time is the ratio of narrow width and length to greater height, symbolizing the prayer's aspiration towards the heavens. The two-tiered nave with windows supports the roof, transitioning from four slopes to a dome vault, which is a unique construction, as the roof does not reflect the ceiling vaults, as noted by historian Nikolai Vasilyevich Valukinsky.

The architectural design of the church is typical for the late 17th and early 18th centuries. The cubic, two-tiered square plan is crowned with five domes. The central drum is light-filled, while the corner drums do not let in light. To the east, the church is adjoined by a three-part apse, equal in width to the square but lower in height. The internal spaces of the deacon's room and altar make up half of the sanctuary, although from the outside, it seems that all parts of the apse are equal. The refectory and bell tower, built later, are executed in the classical style. On the southern wall of the square, there are two plaques, one of which reports on the restoration of the church for the 300th anniversary of the Russian Navy in 1996. The other plaque, installed in 2003, notes that the Russian Navy received its first blessing here before the Azov campaign.

The roof is topped with five domes on small drums with bulbous domes. The decoration of the drums, according to Valukinsky, resembles Moscow churches but is not a copy of them. The central drum is light-filled, while the others are not. The decoration of the central drum traces back to the innovations of Alevis Novy. The cornice under the roof transitions into pilasters adorned with cornices, giving the building an original appearance. The window frames are made in the 17th-century style, but there are no frescoes in the church, and the remnants of previous paintings are hidden under plaster.

In the early 2000s, stands with photographs telling the history of the church were installed. The southeast corner of the refectory is memorial, featuring plaques in honor of sailors who perished on the "Komsomolets" and "Kursk," as well as other commemorative events. Bas-reliefs of Peter the Great and admirals, icons, and the Andreevsky flag, transferred to the church in 2003 along with an icon of Saint Feodor Ushakov, have been installed.

Inside the church, the system supporting the vaults is interesting: arches rest on two pillars in the center of the square. The vaults, except for the central one, are blind, and the drums are not visible from the inside. The decoration of the pillars with baroque elements likely appeared later. The height of the church is 13.1 meters, and the bell tower is 21.4 meters. The wall painting is plastered, and the land area under the church occupies 0.142 hectares.