The church has a traditional cross-shaped form typical of Christian buildings. Above its sloping roof rises a semicircular dome, and the narthex is adorned with a two-tiered bell tower topped with a golden spire. The walls of the Nativity of the Virgin Mary Church are painted in blue and white, harmoniously blending with the blue hue of the Azov Sea.

The history of the church is inextricably linked to the name of Elder Sozontiy Ivanovich. This former merchant and officer, who participated in the Crimean War, later became an elder and possessed the gift of foresight. At a time when the city was still actively being built, mountains of construction debris accumulated on its dumps. One day, Sozontiy came to a meeting of the city deputies and requested a plot of abandoned land to create a men's monastery. Initially, his idea was met with skepticism, but the land was eventually allocated. Sozontiy dug himself a cell, began living as a hermit, and collected funds for the construction of the church. Soon, he was supported by the Orthodox residents of the city, and on September 21, 1904, on the day of the Nativity of the Virgin Mary, the first stone was laid in the foundation of the future church.

Construction was completed in 1907, and a year later, Sozontiy Ivanovich passed away and was buried in the church's crypt.

Henichesk was known for its bell-ringing masters, who would ascend the bell tower during Orthodox holidays, and a magical peal would resonate over the city, reflected in the sea waters. Almost all the residents of Henichesk and the surrounding villages participated in the construction of the monastery, donating money and bringing flour, vegetables, and grain. In the waterless steppe city, which was just beginning to be built, the Nativity of the Virgin Mary Church became a true oasis. At the foot of the hill were a pool, flower beds, gardens, and a stable, while at the top stood the church and refectory. An alley led from the church, lined with fragrant roses, and peacocks with chicks roamed the courtyard. In a small chapel at the entrance, adorned with icons, a lamp burned, and a duty monk read the Psalter. On the other side of the entrance, cells were dug into the ground.

During the revolution and persecution of priests, the monks took in refugees and provided them shelter. Later, under Soviet rule, the monastery's premises were used as a grain storage, and Sozontiy's grave was desecrated. In 1941, services in the church resumed, led by Father Konstantin. He once told the townspeople about the crimes of the communists and the Vinnytsia tragedy, of which he was a witness: he saw the excavations of mass graves where some people were buried alive. When Henichesk was liberated by Soviet troops in 1944, Father Konstantin was arrested on a denunciation, died in prison, and was later posthumously rehabilitated. Soon after his arrest, the church was closed again. During Soviet times, the church premises were used as warehouses, and later a gym for the police was set up there.

Only in 1989 was the Nativity of the Virgin Mary Church returned to the believers. Thanks to their donations, restoration work began. A year later, the dome of the church was restored to its original appearance.