Zvart'nots was constructed at the supposed site of the meeting between King Trdat of Armenia and Saint Gregory the Illuminator as described by the Armenian historian Agathangelos in his account of the conversion of Armenia to Christianity during the 4th century.
Tradition also says that it was built to house the remains of the saint.
The structure was never very stable, and in 1013 strengthening had to be carried out - including the addition of a substantial amount of extra masonry around the middle two columns of each apse, converting them into piers. These consolidations were unsuccessful and the church collapsed shortly afterwards. In the 13th century houses were built around and over the ruins, using some of the fallen church's masonry. Later the ruin site became covered with earth, and at the end of the 19th century all that was visible were some walls on a tall mound. The ruins were excavated in 1906 by Nikoli Marr.