It has a rich historical past, with the medieval Zorats Church, the Tsakhats Kar Monastery and the Smbataberd fortress being located in the vicinity of Yeghegis, as well as a Jewish cemetery from the 13th century.

Yeghegis was a prominent economic and political centre during the Middle Ages, being the seat of the Orbelian Dynasty in the 13th and 14th centuries, which ruled most of Zangezur.

However, after the incursion of the armies of Timur, as well as Turkmen and Persian forces, Orbelian rule ended by the 15th century.

After numerous earthquakes ruined Yeghegis and with the local Armenian population being forcibly exiled into Persia, the village was abandoned.

[2][5] The lost community was rediscovered by Bishop Abraham Mkrtchyan, who, together with his brother, stumbled across the place while making a camp for some orphans from the First Nagorno-Karabakh War.