In the 19th century, a wooden chapel and a small Old Believer prayer house stood on the site of the current Nikolska Church. According to one version, it was built in 1815 with funds from merchant N.D. Tsarsky, which is why it received the unofficial name "Tsarskaya Prayer House." Later, the site passed to the Rakhmanovs, and the community that formed around the prayer house became known as the "Rakhmanov" community. In the 1870s, the chapel acquired an altar and was transformed into a church, which was finally established after 1905 when Old Believers were allowed to officially build their churches.

The project for the new church at Tverskaya Gate, developed by architect I.G. Kondratenko, was approved in 1908, but its implementation began later. The last service in the old building took place on March 16, 1914, after which it was dismantled, and construction of the new church in honor of St. Nicholas the Wonderworker began according to the design of architect A.M. Gurzhienko.

The church is built in the Neo-Russian style, inspired by Novgorod architecture. It has a single dome, with three arches on each side, reinforced with buttresses and pierced with long narrow windows, reminiscent of the Church of the Savior on Nereditsa in Veliky Novgorod. A tented bell tower with an altar in honor of the Prophet Elijah is attached to the church. The facades are decorated with brickwork typical of northern architecture.

World War I slowed down construction but did not stop it. Notable Old Believers contributed funds: S.T. Morozov, E.V. Sherupenkova, P.V. Ivanov, A.E. Rusakov. The church was roughly completed in 1915 and consecrated in 1921 after the interior finishing was completed. Services ceased in 1940-1941, but before the onset of World War II, the basement housed a prayer house for Seventh-day Adventists. During the war, the building was used as a storage facility for Moscow's air defense, and later as a sculpture workshop for the Ministry of Culture of the USSR. It is believed that sculptor S.M. Orlov worked on the monument to Yuri Dolgoruky here. The interior decoration and layout were completely changed, and the church lost its dome and the bell tower's tent.

The first service in the altar of the Prophet Elijah took place in 1995, marking the beginning of the process of transferring the building to the Old Believer community and its restoration. In the 2000s, the historical buildings around the church were demolished and replaced with multi-story buildings of new architecture, creating a new, dissonant backdrop for the church.