On the site of the modern Church of the Prophet Elijah, there was a male Ilyinsky Monastery in the 16th and 17th centuries, the exact date of its founding is unknown. It is suggested that the monastery was built on the site of the pagan shrine of Perun.

The Church of the Prophet Elijah is located on a small elevation. The name "in Kamenye" is related to the fact that during Ivan the Terrible, limestone was stored here, which was used for the construction of the stone wall of the Vologda Kremlin. Historian I.K. Stepanovsky wrote that the stone covered the area from the river to the Vladimir Church in large quantities, remaining in this part of the city until the end of the 18th and the beginning of the 19th centuries. Over time, the unused stone gradually sank into the ground, and only in some places was it visible.

The cold Ilyinsky temple, along with the warm temple of Varlaam Khutynsky, constituted one parish. In the late 19th and early 20th centuries, the parish was small, no more than a hundred people. In the early 1920s, the church passed to the Renovationists. In 1924, the community of the Ilyinsky Church removed the Renovationist priest Alexander Sakharov and unanimously elected Archpriest Alexei Uglicky as the rector, who had previously served in the Assumption Women’s Monastery and supported the Patriarch. On February 24, 1930, the authorities of Vologda decided to close the Ilyinsky Church for worship. The ancient icons of the church were transferred to museum funds. In the 1930s, the church housed an archive, and in the 1950s and 1970s, a book depository.

By a resolution of the Council of Ministers of the RSFSR, the ensemble of churches of the former Ilyinsky Monastery, including the Church of Varlaam Khutynsky and the Church of the Prophet Elijah in Kamenye, was placed under state protection as a cultural heritage site of federal significance. Currently, it houses the federal state cultural institution "All-Russian Artistic Scientific Restoration Center named after Academician I.E. Grabar."