The Bulgarian minority of the Ottoman Empire used to pray at the churches of the Fener Orthodox Patriarchy. With the increase in Bulgarian nationalism, Bulgarian community built their own church in the 19th century. First, a small wooden church was built on the shore of the Golden Horn between Balat and Fener squares where the current church is located, but later this was developed into a larger building. An iron frame was chosen over concrete due to the weak foundations of the site. Hovsep Aznavur, an Armenian Istanbulite, prepared the construction plans. An international competition was conducted to produce the prefabricated parts of the church. An Austrian firm, R. Ph. Wagner, won the competition.

The prefabricated parts were produced in Vienna and transported to Istanbul by ship along the Danube and through the Black Sea. After one and a half years, it was completed in 1898. The main skeleton of the church was made of steel and covered by metal boards. All the metal pieces were attached together with nuts, bolts, rivets or welding. Its architectural style is inspired by the Neo-Gothic and Neo-Baroque movements.