Makarov took control of the project and invited Vasily Kosyakov (1862–1921), already a renowned master of Neo-Byzantine architecture.
The process of this choice remains undocumented, however, Kosyakov had worked for the Navy before as the architect of church of Our Lady the Merciful in Saint Petersburg.
Kosyakov, still in his twenties, had perfected the optimal proportions of a single-dome, four-apse Byzantine design; his 1888–91 drafts of a church in Astrakhan (itself based on Our Lady the Merciful) were reused all over the Empire.
Vasily's younger brother and partner Georgy Kosyakov (1872–1925) was a talented graphic artist; he worked on interiors and finishes while Vasily handled overall and structural design.
Makarov personally instructed Kosyakov that the cathedral must accommodate 5,000 worshippers and follow the historical Byzantine canon.

In 1900–1, Vasily Kosyakov travelled to Istanbul and Greece to refresh his understanding of genuine Byzantine art.
 In April 1901, he presented two preliminary drafts to the Commission of the Navy; the selected draft was approved by Nicholas II 21 May 1901.
Kosyakov departed from his preferred proportions of a tall cathedral with a relatively small main dome; instead he opted for a wide (26 meters) but relatively low dome in line with the proportions of Hagia Sophia.
The reason for this change remains undocumented.
One version attributes it to interference by Makarov.
The admiral once was an attache in Istanbul and was well aware of the genuine Byzantine tradition.
Another likely version links the change to direct influence of professor Nikolay Sultanov, Kosyakov's teacher at the Institution of Civil Engineers, leader of Russian Revival school.
In 1895–1904, Kosyakov was managing the construction of Cathedral of Saints Peter and Paul in Peterhof designed by Sultanov.

By 1903, Kosyakov brothers produced a complete album containing nearly a thousand graphic sheets detailing the structure, exterior and internal design of yet unbuilt cathedral.
Physically, the graphics were executed by Georgy Kosyakov.
Plan, structure, external outline is credited to Vasily Kosyakov; detailed artwork of interior finishes to Georgy.
Interior features were clearly influenced by Art Nouveau, skillfully integrated into a Byzantine shell and complemented with modern engineering systems.
Vasily Kosyakov’s layout also demonstrates influence of Romanesque architecture, notably in the twin belltowers by the sides of the main portal — an extremely uncommon feature in Russian practice.
Makarov took control of the project and invited Vasily Kosyakov (1862–1921), already a renowned master of Neo-Byzantine architecture. The process of this choice remains undocumented, however, Kosyakov had worked for the Navy before as the architect of church of Our Lady the Merciful in Saint Petersburg. Kosyakov, still in his twenties, had perfected the optimal proportions of a single-dome, four-apse Byzantine design; his 1888–91 drafts of a church in Astrakhan (itself based on Our Lady the Merciful) were reused all over the Empire. Vasily's younger brother and partner Georgy Kosyakov (1872–1925) was a talented graphic artist; he worked on interiors and finishes while Vasily handled overall and structural design. Makarov personally instructed Kosyakov that the cathedral must accommodate 5,000 worshippers and follow the historical Byzantine canon.
In 1900–1, Vasily Kosyakov travelled to Istanbul and Greece to refresh his understanding of genuine Byzantine art.  In April 1901, he presented two preliminary drafts to the Commission of the Navy; the selected draft was approved by Nicholas II 21 May 1901. Kosyakov departed from his preferred proportions of a tall cathedral with a relatively small main dome; instead he opted for a wide (26 meters) but relatively low dome in line with the proportions of Hagia Sophia. The reason for this change remains undocumented. One version attributes it to interference by Makarov. The admiral once was an attache in Istanbul and was well aware of the genuine Byzantine tradition. Another likely version links the change to direct influence of professor Nikolay Sultanov, Kosyakov's teacher at the Institution of Civil Engineers, leader of Russian Revival school. In 1895–1904, Kosyakov was managing the construction of Cathedral of Saints Peter and Paul in Peterhof designed by Sultanov.
By 1903, Kosyakov brothers produced a complete album containing nearly a thousand graphic sheets detailing the structure, exterior and internal design of yet unbuilt cathedral. Physically, the graphics were executed by Georgy Kosyakov. Plan, structure, external outline is credited to Vasily Kosyakov; detailed artwork of interior finishes to Georgy. Interior features were clearly influenced by Art Nouveau, skillfully integrated into a Byzantine shell and complemented with modern engineering systems. Vasily Kosyakov’s layout also demonstrates influence of Romanesque architecture, notably in the twin belltowers by the sides of the main portal — an extremely uncommon feature in Russian practice.
Kronstadt Naval Cathedral