It was founded around 1330 by a Tatar convert, Prince Chet, whose male-line descendants included Solomonia Saburova and Tsar Boris Godunov, and is dedicated to St. Hypatios of Gangra.

The main theory considers Tatar Murza Chet, baptized as Zachary, to be the founder of the Ipatievsky Monastery.

The legend says that he was miraculously cured from a disease by a vision of the Virgin Mary and St. Philip and St. Hypatius, and decided to build the monastery as a sign of gratitude.

During the Time of Troubles in Russia, the Ipatiev Monastery was occupied by the supporters of False Dmitriy II in the spring of 1609.

A private house of Mikhail Romanov was restored on the orders of Tsar Alexander II, though the authenticity of the reconstruction was questioned by Konstantin Pobedonostsev .