In 1799, the construction of a single-altar stone church in honor of the Nativity of the Virgin Mary began, completed in 1800 with funds from Russian merchants. Because of this, it was also called "Old Merchant Church." The construction of the church was overseen by Archpriest Karp Pavlovsky. The height of the temple is 38 meters, and its walls are made of hewn shell stone. Initially, the columns were gilded. In 1828, two new side altars were added to the main altar in honor of the Nativity of the Blessed Virgin Mary: the left dedicated to the holy emperors Constantine and Helena, and the right in honor of St. Mitrophan, Bishop of Voronezh. That same year, the church was granted the status of a Cathedral. In 1835, when the question of naming the street where the Cathedral is located was being decided, H.G. Avtonomov suggested to Admiral M.P. Lazarev to name it Christmas Street in honor of the Nativity Cathedral.

In 1874, a church-parish guardianship was established at the cathedral, of which the rector of the Kronstadt Cathedral, Archpriest Ioann Sergiev, now known as Saint Righteous Ioann of Kronstadt, became an honorary member in the early 20th century.

The temple is located in the historical part of Mykolaiv, known as "Gorodovoy," at the intersection of Christmas Lyagina and Merchant Potemkin streets. In 1922, during the confiscation of church valuables to aid the starving, the cathedral community donated 172 kg of silver. On January 31, 1930, the authorities removed the bells weighing 10.2 tons of non-ferrous metal, and on November 8, 1936, the cathedral was closed. In the pre-war years, the building was used as a garrison House of the Red Army and Navy, and after the war, it became the "Officers' House."

In the early 1990s, the cathedral was handed over to the Ukrainian Orthodox Church of the Moscow Patriarchate and has since become a beloved place for many residents. It houses the relics of St. Martyr Sergius, who suffered for his faith, as well as a part of the relics of St. Righteous Feodor Ushakov.