The exact year of the construction of the first church in Yunakovka is unknown. However, Bishop Filaret had documents confirming that in 1709 there was already a temple in Yunakovka dedicated to Saint Nicholas the Wonderworker. According to a description from 1785, the church was large, wooden, single-altar, five-domed, with extensions on four sides, giving it a cross-shaped form. All five domes were gilded. There was a separate wooden bell tower with six bells, the largest of which weighed 106 poods. Two kiots and a tin chalice have survived from the old church.

The first church in Yunakovka existed until 1793. In that year, it was permitted to dismantle the dilapidated wooden church and build a new stone one in its place with three altars: in the name of Saint Nicholas the Wonderworker, Archangel Michael, and in honor of the Nativity of the Blessed Virgin Mary. The main altar was dedicated to the Nativity of the Virgin Mary, and since then the church has been called "Nativity of the Virgin Mary Church." This majestic temple was built exclusively on donations from parishioners over 13 years and was completed in 1806.

In 1823, the old bell tower was dismantled, and a new one was built thanks to Priest Korniliy Krasnokutsky, who donated 10,000 rubles for this purpose. The final finishing of the bell tower was completed in 1827 by the efforts of Priest Vasiliy Maksimovich Nikolsky. The bell tower housed a large bell weighing 206 poods with the inscription: "This bell was made by the efforts and care of the honorable protoiereus V. Nikolsky in 1857."

In 1874, a warm church in honor of the Three Hierarchs was arranged in the lower basement of the temple. Vasiliy Maksimovich Nikolsky served in the Yunakovka church from 1826 to 1882, leaving a good memory of himself. He was an tireless pastor until old age. The church has long housed a miraculous icon of Saint Nicholas, adorned with a silver-gilded robe with precious stones and enamel. This was a gift from the owners of the Yunakov estate, N. I. and M. M. Leshchinsky.

The exact time of the appearance of this icon is unknown, but there is a tradition that it appeared in Yunakovka before the construction of the first church and was temporarily located in the Loknyansk church. Later, a wooden chapel was built for the icon, and then it was transferred to the first church. Many miracles associated with this icon are recorded in the church ledger. For example, in 1770, three merchants from Kursk, fleeing from robbers, called for help from Saint Nicholas, and the robbers were blinded, not seeing them.

The Nativity of the Virgin Mary Church also houses a revered icon of the Akhtyr Mother of God with a silver-gilded robe. The robe bears the inscription: "This robe was made in memory of deliverance from drought through the prayers of the Mother of God, the diligence of clergymen and parishioners in 1892." In the spring of 1892, drought threatened the harvest, but after special prayers before the icon, rain began, which lasted for three days and saved the crops.

In recent years, the Nativity of the Virgin Mary Church in Yunakovka was under the jurisdiction of the Kyiv Patriarchate. After legal proceedings in 2010, the church was transferred to the Sumy Diocese of the Ukrainian Orthodox Church. The consecration of the temple took place on June 3, 2010, by Bishop Evlogiy of Sumy and Akhtyr. Currently, the church is undergoing restoration and renovation.