The first mention of the men's monastery in the settlement of Mstyora dates back to 1628-1629. It was located on land owned by the Romanov princes. In the 17th century, the Ivanovsky women's monastery with the churches of John the Merciful and Philip the Metropolitan was nearby.

In 1683, the wooden Bogoyavlensky church of the monastery fell into disrepair, and princes Fyodor, Andrey, and Mikhail Romanov, having received permission from the Metropolitan of Suzdal, Hilarion, built a five-domed stone church of the Epiphany, consecrated in 1687-1688. A burial vault for the Romanov princes was also established here.

The Vladimir church of the monastery is first mentioned in 1734. The bell tower, known since 1710, had five bells and a clock.

On June 7, 1869, a chapel of Alexander Nevsky was laid at the Vladimir church. In October 1873, a hurricane damaged the bell tower's spire, leading to major repairs, after which the building was completely rebuilt.

In the early 1930s, after the monastery was closed, a museum of painting, church, and folklore antiquities was established here. In 1953 and 1973, the Bogoyavlensky church was used as a warehouse.

On September 24, 1999, with the blessing of Archbishop Evlogy of Vladimir and Suzdal, the Bogoyavlensky men's monastery was revived. A community of four was formed, with Hieromonk Ilya Ivanov as the abbot, later succeeded by Hieromonk Sergey Titov. In September 2007, after Hieromonk Sergey Titov was transferred to Zosimova Pustyn, Hieromonk Avraamy Lukiyanchuk was appointed as the abbot, elevated to the rank of igumen in 2008.