This church was the second of the parish churches built in the White City. Its name indicates a close connection with the Astrakhan merchant class and the trading courtyard in Astrakhan. Saint Nicholas the Wonderworker, the patron of trade and navigation, was particularly revered among merchants, which contributed to the construction of the church in his honor near the Russian trading courtyard and river docks, where goods were actively unloaded and loaded. The exact time of the original church's construction is unknown, but it can be asserted that it was built soon after the appearance of the trading courtyard in Astrakhan. The chronicler reports that in 1599, during a fire, the trading courtyards burned down, including the Russian, Bukhara, and Gilan courtyards, confirming the existence of the trading courtyard at the end of the 16th century. It is likely that the first wooden Nicholas church was built in the early 17th century, with the first mention of it dating back to 1628.

In the early 18th century, the construction of a new stone church began. Metropolitan Sampson, the initiator of the construction, convinced Astrakhan merchants to finance this pious endeavor. Although the metropolitan did not live to see the completion of the construction, the main works were finished by his death in 1714. Under his successor, Bishop Joakim, on November 5, 1714, the left chapel in honor of St. George the Great Martyr was consecrated. Further work continued for a long time, and only on June 23, 1721, was the main altar consecrated in the name of Saint Nicholas, possibly in connection with the planned visit of Emperor Peter I to Astrakhan in 1722. Governor Artemy Volynsky tried to tidy up the city for the emperor's arrival. In June 1755, a chapel was arranged in the church's refectory on the right side in honor of the icon of the Mother of God "Joy of All Who Sorrow" as a vow by Mikhail Fyodorovich Gnevashov. The chapel was consecrated by Archimandrite Aaron on November 12 of the same year. Over time, the church underwent several reconstructions and renovations.

In 1971, the executive committee of the Astrakhan City Council, citing a report on the technical condition of the church building conducted by engineer O.K. Bar-Ramensky, and considering the emergency state of the structures, decided to allow the regional trade administration to dismantle the building of the former Nikolskaya church on Khalturina Street. The city council's conclusion contained many falsehoods, as engineer Bar-Ramensky insisted on preserving the church during major repairs. The church could have stood for a long time if not for the planned construction of a shopping center with a restaurant in its place. The destruction of the church took a long time, as the massive walls were difficult to bring down. Believers from Astrakhan collected pieces of plaster with paintings, taking them home as relics. By 1974, not a trace of the church remained.

The Guest-Nikolai church became the last of the Orthodox churches destroyed during the period of communist rule. Now, a modern building of a central department store made of glass and concrete stands in its place.