Agulis was known from antiquity as an Armenian cultural center of trade and crafts being a part of the Vaspurakan province of the Kingdom of Armenia.

Numerous sixteenth-century sources spoke of it as a thriving town that maintained strong commercial links with India, Russia, Safavid Persia and Western Europe.

[3] The monastery was an important center of learning whose alumni included the merchant and traveler Zakaria Aguletsi, A. Araskhanyan, animal breeder Avetis H. Kalantar, and L.

[4] In the spring of 1919, the First Republic of Armenia extended administrative control over the region of Sharur-Nakhchivan, with Agulis being made the centre for the sub-district of Goghtan.

But in the summer of the year, a Muslim insurgency broke out against Armenian rule, and in August the region came under the control of the newly appointed commissar of Ordubad, Abbas Guli Bey Tahirov.

[5] Agulis pledged its loyalty to Tahirov, although in the following months, its inhabitants faced a growing food crisis and were not allowed to leave the town.

The plight of its inhabitants worsened when, in November of that year, the Azerbaijan Democratic Republic unsuccessfully attempted to wrest the region of Zangezur from Armenian control.

[3] It, along with other Armenian churches, were destroyed by Azerbaijan state authorities toward the end of the 1990s,[9] at some point between 1997 and 2009[10] On May 15, 2014, a mosque was constructed on the place of the monastery complex.