The architectural appearance of the temple resembles Armenian churches of the 13th-14th centuries: a square building with a dome on an octagonal drum and narrow windows. Later, the church was rebuilt: a spacious area was added at the main entrance, divided by columns into three naves, covered with vaults and arches on consoles. This allowed the temple to accommodate more parishioners. After passing through a somewhat gloomy annex, the faithful entered a bright domed hall, decorated with figures of John the Baptist and Nicholas the Wonderworker made of stone. These sunlit sculptures made an impression. In the upper part of the apse, there was an image of Christ and the twelve apostles.

Over time, buildings deteriorate, but at the end of the 19th century, Bishop Germogen of Taurida and Simferopol described the interior of the church as follows: "The church is remarkable for its ancient images on the walls: the Savior in the heavenly place, on the sides the 12 apostles, John the Baptist with the lamb above the altar, Saint Nicholas with a book on the southern wall, the face of the Lord under the dome, Saint George on horseback at the entrance. The temple is small, but sturdy."

The temple was painted with frescoes, fragments of which have survived. In 1927, a restoration commission, which included artist and art historian I.E. Grabar, examined the medieval churches of Feodosia. Grabar suggested that some frescoes of the Church of John the Baptist might have been created by the Byzantine painter Theophanes the Greek, who worked in Russia in the 1370s. His icons and frescoes have survived in the Annunciation Cathedral in Moscow and the Church of the Savior on Ilyin Street in Novgorod.

An historical event is associated with the church: in the autumn of 1474, the Russian traveler Afanasy Nikitin arrived in Kaffa, returning from India. In "Journey Beyond Three Seas," he wrote that he arrived in Kaffa nine days before the Feast of Philip. The legend states that he visited the Church of John the Baptist and prayed there, rejoicing at his return home after living among Buddhists and Muslims.

In 1475, the Turks captured Kaffa, and Islam became the main religion, although churches of different confessions remained in the city. Over time, the Church of John the Baptist fell into disrepair and became known as the Quarantine Church. In 1887, Bishop Germogen wrote about the Quarantine Church, built of wild stone in honor of the Iveron Icon of the Mother of God. In 1858, priest Nikolai Tregubov revived it with the help of benefactors, and in 1875, Rukavishnikov painted the church and donated three icons.

In 1906, the artist Konstantin Bogaevsky and Josephine Durante were married in this church. Bogaevsky, a well-known Russian artist, was born in Feodosia and lived in Quarantine, where his workshop was located. The church was his favorite. During the revolution, about 7,000 White soldiers and officers were shot near the church.

In the 1930s, the church was closed and abandoned. Despite the establishment of a historical and architectural reserve, it began to deteriorate. Due to disputes, restoration work was not carried out for seven years, and water damaged the frescoes through holes in the roof. However, thanks to the efforts of concerned individuals, including architect Valeryzamekhovsky, the church was saved. Drainage work was carried out, the ground level was lowered, and the courtyard was paved with stone. Future parishioners helped by cleaning up debris and beautifying the courtyard. The restoration was completed in 1996, and the church was returned to the faithful.