The church is estimated to have been built between 1583 and 1604, and depicts Christ Pantokrator and the Apostles’ portraits on its middle nave and volutes surfaces.

The church has been documented by the Russian traveller Tryphon Korobeinikov. It was ravaged by fire in 1695, renovated in 1725 and burnt again in 1796. The community of the church, after its last reconstruction in 1804, was mainly made up of sailors. The church was seized after the anti-Greek riots of 1956 and has been in the Turkish Orthodox Archdiocese since 1963. Another fire in the 21st century destroyed more of its parts.

The church takes the form of a three-nave basilica. The Ayazma was built in 1867 in its narthex. On the upper part of the iconostasis are scenes from the story of Jesus. On the lower part, other saints are depicted. On the surface of the ambo facing the middle nave, Jesus and the four writers of the Gospels are depicted. A ship model hanging from the middle nave represents St Nicholas.

Cornucopia contributor Pat Yale writes about the hidden churches of Karaköy, which includes the Church of St Nicholas, on her blog.