Until it was inaugurated in 1849, the Bulgarian Orthodox Christians who were living under the reign of the Ottoman Empire, used to pray at the Phanar Orthodox Patriarchate. However, the Bulgarian nationalist movement in the 19th century decided to separate from them, and as a result of the attempt, the Bulgarian St. Stephen Church was built in the Balat district of Istanbul. The wooden church was first built at the same place as the iron one, but it was nonetheless damaged by a fire. The iron church was built with prefabricated materials due to the poor ground conditions.It was designed by the Istanbul-based Ottoman Armenian architect Hovsep Aznavour in a combination of Neo-Byzantine and Neo-Baroque influences.
The Iron Church was the conclusion of 19th-century prefabricated iron church experiments. So many iron churches were built and sent to countries like Australia, Peru, and the Philippines, designed by French engineer Gustave Eiffel, who was also the creator of the Eiffel Tower in the era. It has been known that the weight of the prefabricated elements of the church is 500 tons; they were fabricated in Vienna and transported to Istanbul by sea between 1893 and 1896. The church is one of the survival iron churches that left fron 19th century.