Before the design and construction of the Orthodox church, plans were drawn up in the 1820s by architect Carl Ludvig Engel for a church on the same site, but designed in the neoclassical style in keeping with the rest of buildings at the fortress and the buildings in the capital city, Helsinki.

During the 1920s, it was decided to give the church an extensive renovation for structural repair as well as incorporation of a more Western design.

The design competition was won by architect Einar Sjöström, and the finished church was reconsecrated on 28 April 1929.

Additional renovations have been made in the 1960s (after the church was turned over to the Evangelical Lutheran Parish Union of Helsinki), and again in the late 1980s and 1990s in preparation for the 250th anniversary of Suomenlinna in 1998.

The Suomenlinna Church is still a very popular wedding site and one of the first landmarks for people arriving in Helsinki by sea.