In 1899, the St. Nicholas Cathedral was consecrated in Eupatoria, but this was not enough for the Orthodox residents of the city. In 1901, at the request of the local Greek community, the Eupatoria City Duma allocated a plot of land measuring 600 square fathoms for the construction of a new church free of charge. Six years later, city architect Adam Ludwigovich Heinrich prepared a project for this purpose.

In 1911, the site for the construction of the church in honor of the prophet Elijah was consecrated, funded by the Greek community. A significant sum was donated by shipowner Panait Davydov, who also oversaw the construction. However, funds were coming in slowly, and the community appealed to the Duma for a subsidy of 5,000 rubles. The city mayor, Semyon Ezrovich Duvan, agreed to pay the subsidy in installments and personally donated 400 rubles and a bronze chandelier. For his assistance in the construction of the church, Duvan was awarded the Cross of the Holy Savior by the King of Greece. Construction began on June 6, 1911, and continued until 1916 under the guidance of architect Heinrich. The building was constructed from local limestone. In the corners between the arms of the church were four symmetrical structures: the altar, the deacon's room, the choir loft, and the staircase to the choir. On June 30, 1918, the church of the prophet Elijah opened for worshippers, and the consecration was conducted by Archbishop Dmitry of Taurida, Prince Abashidze. The interior decoration of the temple was completed almost ten years later, during the period of persecution against the Church.

After the revolution, the church remained active, but it did not escape trials. In 1922, church valuables were confiscated by the decree of the All-Russian Central Executive Committee. In 1936, bell ringing was prohibited in Eupatoria, and then the church was closed, transferring the building to the Committee of Physical Culture and Sports. The rector, Archpriest Eleazar Spiridonov, wrote to the Greek consul in Moscow about this and was arrested, receiving a five-year camp sentence. He was sent to Kolyma, where he died six months later. In the same year, the authorities terminated the contract with the Greek community due to the impossibility of repairing the building. During the Great Patriotic War, the church was reopened, and the service was led by Ivan Ulezko. However, in the late 1950s, the church was closed again due to the emergency condition of the bell tower. Attempts were made to demolish it using military equipment, but only the upper tiers were dismantled in 1959. The building was again used as a gym, and the icons of saints were whitewashed.

In the late 1980s, believers began work to return the church. In December 1989, the Eupatoria Executive Committee transferred the building to the religious community. On May 2, 1990, Archbishop Varlaam consecrated the church. Thanks to rector Georgy Kunitsyn, the bell tower and altar were restored, and the icons were returned. The icons and frescoes were created by artists Ananiy and Ivan Melnychuk. For the anniversary of Eupatoria in 2003, the bell tower was restored, and a new bell was installed, cast at the enterprise 'Blagovest-1.'

The Greek church, unlike the elaborate St. Nicholas Cathedral, looks simple: smooth walls made of shell rock and concise facades. The temple is built in the Greek-Byzantine style and has a cross shape. It rises on a high pedestal, giving it an imposing appearance. The dome stands on an octagonal drum with pediments. The decoration includes pilasters and arches with stained glass. To the east is a five-sided apse, and the main entrance is framed by an arch on half-columns. The three-tiered bell tower is significantly taller than the dome. On the apse, there is a mark from shrapnel fired from the Turkish cruiser 'Midilli' on April 24, 1916.