In the early 17th century, a wooden church dedicated to the holy Zosima and Savvatiy of Solovki stood on the site of the current temple. In 1712, it was replaced by a stone structure that has survived to this day. The construction of the Nicholas Church is associated with Queen Evdokia Lopukhina, who was exiled in 1698 by her husband, Tsar Peter I, to the Suzdal Protection Monastery. With her own funds, Evdokia built a winter church of St. Nicholas the Wonderworker opposite the Holy Gates of the monastery and added an altar in honor of St. Alexius, the heavenly patron of her son, Tsarevich Alexei, who was then the heir to the throne. The Nicholas Church, built in 1712, along with the summer church of Peter and Paul, erected in 1694, formed an architectural ensemble. This ensemble became a model for many "paired" churches built in Suzdal from the 17th to the 19th centuries.

The Nicholas Church, like all winter churches in Suzdal, is characterized by simple architecture and modest decor. Its composition resembles the large single-domed churches of Suzdal. The church building is cubical, topped with a four-pitched roof, on which rises a tall slender drum with an onion dome. The facade is adorned with zakomaras. A semicircular apse adjoins the church on the eastern side, while a small porch is located on the western side. The Nicholas Church has undergone numerous reconstructions, but in 1954, its original appearance was restored.