Originally built in 1108-1113  the by Svyatopolk Izyaslavovych, a grandson of the Great Duck Yaroslav the Wise. The monastery comprises the Cathedral itself, the Refectory of St. John the Divine, built in 1713, the Economic Gates, constructed in 1760 and the monastery's bell tower, which was added c. 1716-1719. The exterior of the structure was rebuilt in the Ukrainian Baroque  style in the 18th century while the interior remained in its original Byzantine style. The original cathedral was demolished by the Soviet authorities in the 1930s, but was reconstructed and opened in 1999 following Ukrainian independence in 1991.
One reason for building the church may have been Svyatopolk's recent victory over the nomadic Polovtsiqns (Cumans) as Michael the Archangel was considered a patron of warriors and victories. In 1906, a medieval hoard of silver and gold jewellery was discovered in a metal casket on Trekhsvyatytelska Street (Street of the Three Saints), opposite the gates of St. Michael's Golden-Domed Monastery. Gold jewellery from the hoard is now in the Metropolitan Museum of Arts, New York while the silver jewellery and two ingots are in he British Museum, London. The hoard is dated to the 11th-12th centuries and was probably hidden at the time of the Tartar invasions and the Sack of Kiev in 1240.

During the Mongol invasion in 1240, the monastery is believed to have been damaged seriously. The Mongols damaged the cathedral and removed its gold-plated domes. The cloister subsequently fell into disrepair and there is no documentation of it for the following two and a half centuries. By 1496, the monastery had been revived and its name was changed from St. Demetrius' Monastery to St. Michael's after the cathedral church built by Sviatopolk II. After numerous restorations and enlargements during the sixteenth century, it gradually became one of the most popular and wealthiest monasteries in Ukraine. In 1620, Iov Boretsky made it the residence of the renewed Orthodox Metropolitan of Kiev, and in 1633, Isaya Kopynsky was named a supervisor of the monastery.

The monastery enjoyed the patronage of hetmans and other benefactors throughout the years. The chief magnet for pilgrims were the relics of Saint Barbara, alleged to have been brought to Kiev from Constantinople in 1108 by Sviatopolk II Iziaslavych's wife and kept in a silver reliquary donated by Hetman Ivan Mazepa. Although most of the monastery grounds were secularized in the late eighteenth century, as many as 240 resided there in the nineteenth and twentieth centuries. The monastery served as the residence of the bishop of Chernigiv after 1800. A precentor's school was located on the monastery grounds; many prominent composers, such as Kyrylo Stetsenko and Yakiv Yatsenevych, either studied or taught at the school.

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