The church erected in 1896–1897 on the site of the old graveyard in Haapsalu was dedicated to Alexander Nevsky. A Moscow style tent roof crowned with a small onion dome and a vestibule with a belfry were added according to the project by architect A. F. Krassovsky from St. Petersburg.

The original iconostasis based on the drawings by academician Šaub is now at the orthodox church in Kiviõli, where it was transferred in 1962 after the church was closed.

The church was used as a venue for funerals all year round. A stove was built in the church in the middle of the 20th century and then it was used as the winter church. At the moment the Haapsalu Mary Magdalene (Alexander Nevsky) parish of the Estonian Orthodox Church of Moscow Patriarchate uses the church.