In the 17th century, the area beyond Arbat, adjacent to the Moscow River, became an important construction center. Here was the State Wood Chip Yard, where log cabins for wooden buildings were made. The proximity to the river was particularly significant, as firewood and construction timber were delivered by it. In this area, a settlement of carpenters formed, who likely became parishioners of the first wooden church in honor of Saint Nicholas the Wonderworker, first mentioned in 1649. Later, in 1668, among the benefactors of the church were royal cooks, bakers, and guards. In 1686, by the order of Patriarch Joakim, the construction of the stone Nikolskaya Church began, the main part of which has survived to this day.

The architecture of the church is typical for the 17th century: it is elongated from west to east, starting with the bell tower and refectory, and ending with the main volume with altar projections. However, the facades are decorated in the Naryshkin Baroque style: the window frames are adorned with "broken pediments," the corners are highlighted by triple columns, and a cornice runs under the kokoshniks. The heads of the church are topped with large crosses, the central one of which is crowned, symbolizing the attention of the Romanov dynasty, which made contributions to the Church of Nicholas on Shchepakh.

In addition to the chapel of the apostles Peter and Paul, since 1773, there was another chapel in the refectory, in honor of Saints Simeon and Anna, created with the funds of local resident Anna Ivanova. After the French occupation of Moscow in 1812, when the church suffered from fire and looting, the building was partially rebuilt. The interiors featured an iconostasis from the late 17th century, corresponding to the time of the stone church's construction.

In the early 20th century, the Church of Saint Nicholas the Wonderworker on Shchepakh was well-known in Moscow. In 1908, the funeral of Father Valentin Amphiteatrov, the former rector of the Assumption Cathedral in the Kremlin, took place here. However, after the revolution, the church faced a sad fate: closed in the 1930s, it lost its domes and the top of the bell tower, the facades were plastered, the interiors destroyed, and the interior space divided into floors. The building, raised and rebuilt, completely lost its historical appearance, turning into a factory workshop of the "Artistic Engraving" association. Only in the 1970s did the cleaning of the facades reveal that the 17th-century decor had been preserved under the plaster. In 1994, the building was handed over to the church community, after which a long restoration began, completed in 2008. Today, the Church of Nicholas on Shchepakh has regained its historical appearance.