The monastery is located on the territory of the ancient citadel of Pereyaslav. According to the "Tale of Bygone Years", in 1072, the abbot Nikolai of Pereyaslav participated in the transfer of the relics of the holy princes Boris and Gleb to Vyshgorod. This event is considered the first mention of the monastery of Saint Archangel Michael in Pereyaslav. Archbishop Filaret Gumilevsky suggested that later Nikolai became the bishop of Pereyaslav and is mentioned in the "Kyiv-Pechersk Paterik" as a native of the Kyiv-Pechersk Lavra.

In 1089-1090, the "Tale" reports the consecration of a new church of Saint Archangel Michael, built during a large stone construction project led by Metropolitan Ephrem. He also erected the church of Saint Theodore Stratilates, the temple of Saint Andrew the First-Called, the stone walls of the Episcopal courtyard, and a public bath. According to the "Paterik", Ephrem began his ministry as one of the first monks of the Kyiv-Pechersk Lavra, temporarily lived in Constantinople, and his relics rest in the Near Caves of the Lavra.

From the late 11th century until the Mongol invasion in 1239, the monastery served as the residence of the archbishops of the Pereyaslav diocese. At that time, Pereyaslav, Kyiv, and Chernihiv were the main cities of Rus, and the archbishops of Pereyaslav held the title of metropolitans but were subordinate to the Kyiv metropolitan. The Laurentian Chronicle notes under the year 1089: "Previously, there was a metropolitanate in Pereyaslav." Among the notable bishops of Pereyaslav were Silvester, abbot of the Kyiv-Vydubitsky Monastery, and Simeon, who was killed during the capture of the city by the Mongols. Other archbishops participated in important events in the church life of Rus.

In the 12th century, chronicles mention the Holy Michael Church as a place of princely prayers and burials. Here were buried the sons of Monomakh and the nephew Rostislav. In 1149, Prince Iziaslav prayed here before a battle.

In the 17th century, the memory of the monastery was preserved in the form of a wooden church. In the first half of the century, the Holy Michael Church is mentioned, and between 1649-1666, the Cossack Fedor Loboda built a new church of Saint Archangel Michael.

In the 18th century, a new complex was built on the site of the monastery. In 1711-1713, the stone Holy Michael Church and other buildings were erected. In 1734, the monastery suffered from a fire but was restored. In 1743-1750, a new stone church was built. In 1786, the monastery became a parish.

From 1713 to 1786, the relics of Macarius of Ovruch were kept here. In 1713, they were transferred from the Resurrection Church, and in 1750, to the new church. In 1786, the relics were returned to the Ascension Monastery.

From 1768 to 1771, the monastery was managed by Abbot Melchisedek Znachko-Yavorsky, later an archimandrite.

In the 19th century, the study of the monastery's monuments began. In 1827, the church and bell tower were included in the list of protected structures. In 1840, Alexander Annenkov discovered the foundations of the ancient church. In 1845, Taras Shevchenko sketched the church, and in 1850, it was renovated.

During the Soviet era, the parish was abolished. In 1949 and 1953-1954, Mikhail Karger studied the remains of the ancient church. In the 1950s, the church faced destruction, but Mikhail Sikorsky opened an ethnographic exhibition here. In 1974, Sikorsky and other researchers cleared the foundations of the church. In 1979, a pavilion was built over the northern foundations, and in 1982, the Museum of Architecture of Ancient Pereyaslav was opened.

In July 2007, a small tent church of Saint Archangel Michael was installed near the ancient church. In 2011, the Holy Synod of the UOC blessed the opening of the men's monastery.