In 1191, Grand Prince Vsevolod Yuryevich founded a men's monastery in Vladimir, choosing a location on the eastern side, near the Ivanov Gates. Chronicles indicate the foundation in 1191-1192: "In that year, Grand Prince Vsevolod laid a stone church in the city of Vladimir for the Nativity of the Holy Mother of God on August 22 under Bishop Ioann." The prince and his court were present at the laying. The monastery established a communal life, and the prince granted it numerous villages and lands. The monastery was led by igumens, with Simon and Mitrophan later becoming bishops of Vladimir.

From 1230, the monastery was headed by archimandrites. The Nativity Monastery became known as the Great Archimandrite and was considered the first among Russian monasteries until the reign of Ivan Vasilyevich. From the mid-13th century to the early 14th century, all-Russian metropolitans, who moved their see from Kyiv to Vladimir, resided in the Nativity Monastery, which was their cathedral.

On July 25, 1723, Archimandrite Sergey received an order from Emperor Peter I to transfer the relics of Saint Prince Alexander Nevsky to St. Petersburg. The last archimandrites, Pavel and Platon Petrunkevich, were members of the Holy Synod. In 1561, by the order of Tsar Ivan Vasilyevich, primacy was given to the Trinity-Sergius Monastery, and the Vladimir Nativity Monastery became second. After the establishment of the Alexander Nevsky Monastery in 1720, it became third, but due to its antiquity and significance, it remained under the direct supervision of metropolitans, patriarchs, and the Holy Synod.

In the early 18th century, the monastery had 64 monks, including two archimandrites, six hieromonks, and five hierodeacons. According to census records, the monastery had 96 courtyards of servants and 13 courtyards of peasants. On July 27, 1744, by the decree of Empress Elizabeth Petrovna, the Vladimir diocese was established, and the monastery became the episcopal residence for Bishop Platon. Until 1764, the monastery was maintained by the income from 7,899 peasant souls. In 1789, after the unification of the Vladimir and Suzdal dioceses, Bishop Viktor moved to Suzdal, and the episcopal residence became a civil institution. In 1797, Bishop Viktor proposed to transfer the Tsar-Constantinov Monastery to Vladimir, but in 1798, by the decree of the synod, it returned to the Nativity Monastery, where Vladimir archbishops have resided since.

On September 5, 1858, Emperor Alexander II visited the monastery and ordered the restoration of the Church of the Nativity of the Most Holy Mother of God to its ancient form, donating 40,000 rubles. In 1859, architect Nikolai Artleben and D. Koritsky demolished the old temple and built a new one. P. D. Baranovsky welcomed the project as the first example of scientific restoration in Russia. In 1924, he visited Vladimir to prevent the demolition of the church. From 1918 to 1991, the territory of the monastery housed departments of the Cheka, OGPU, NKVD, KGB, and a pre-trial detention center. In 1930, the cathedral and bell tower were dismantled at the initiative of the OGPU chief, despite protests from specialists. During the Stalinist repressions, the monastery grounds were used for burying the repressed, as evidenced by a memorial plaque. In 1991, marking the monastery's 800th anniversary, its revival began, and new cathedral and bell tower were built in simplified forms.