The monastery was founded by St. Lukian of Alexandrov on September 10, 1650, at the site where the icon of the Mother of God "Nativity of the Theotokos" appeared in 1594, later known as Lukianovskaya. The first abbot was Lukian himself, born in 1610 in Galich. From the age of eight, he was raised in the monastery under his father's guidance. In 1640, Lukian first visited the future monastery site and took monastic vows there, although he was expelled three times by local residents. In 1646, Patriarch Joseph ordained him a priest at the Chudov Monastery in Moscow. With the support of Moscow merchants, Lukian built the Church of the Nativity of the Theotokos and cells for the monks. In 1654, he founded the women's monastery of the Assumption of the Holy Theotokos in Alexandrov at the request of local merchants. Lukian passed away on September 21, 1655, and his memory is celebrated the following day. His work was continued by St. Cornelius, under whom the monastery became known for its spiritual and architectural appearance. Cornelius led the monastery from 1657 until his death on August 24, 1681. The monastery was supported by Tsars Feodor, Ivan, and Peter Alexeyevich, as well as other members of the royal family. Until the end of the 17th century, all buildings were wooden, but between 1680 and 1684, by order of Tsar Feodor Alexeyevich, a stone refectory church of the Epiphany with a chapel of St. Theodore Stratilates was built. At the end of the century, the construction of stone cells began; in 1690, the Treasury building was erected, in 1696 the Bread cells and Hospital ward, and in 1712 the Cathedral of the Nativity of the Theotokos, consecrated in the presence of the princesses Martha and Theodosia. In 1771, a chapel was built over Lukian's grave between the cathedral and the refectory church. In 1714, a church of St. Catherine was built near the Hospital ward. By 1733, a stone fence with seven towers was erected around the monastery. In 1771, the icon of the Nativity of the Theotokos became famous for a miracle: after a procession with the icon around Alexandrov, the plague epidemic ceased. Since then, the procession has become annual, and the icon gained wide recognition as "Lukianovskaya." In the early 19th century, a new Fraternal building and a hotel were constructed south of the monastery. In 1894, the interior of the Cathedral of the Nativity of the Theotokos was painted.

The monastery owned horse, brick, and tile factories, as well as several mills. The desert had three wooden chapels on the Moscow road and near Pereslavl. In Moscow, there was a dependency of the monastery at the Sretensky gates. In 1922, the monastery was closed, its property was taken away, and some icons and relics were destroyed. The whereabouts of the miraculous icon of the Nativity of the Theotokos remain unknown. The monastery was converted into a nursing home with departments for the mentally ill and the blind. In 1991, Lukian's desert was the first to be revived in the Vladimir diocese. In 1992, the relics of St. Lukian were discovered and are now located in the Church of the Epiphany. The relics of St. Cornelius were found in 1995 and placed in the Trinity Church of the Assumption Women's Monastery in Alexandrov. In 1999, by the blessing of Patriarch Alexy II, an icon "The Abbess of the Holy Mountain Athos" was written for the monastery. By that time, the Church of the Epiphany had been fully renovated. In 2001, the restoration of the Nativity of the Theotokos Cathedral began but was only completed with the restoration of the roof, domes, and cupolas. In 2002, the southern wall, one of the first stone buildings from 1718, was restored. In 2005, one of the seven towers was restored, and in 2011, another one. In early 2008, Archimandrite Dosifei, who had led Lukian's desert for 17 years, was transferred to the Spiritual Mission in Jerusalem. He passed away suddenly on March 13, 2009, from a heart attack. The monastic burial service took place on March 18 at the Holy Danilov Monastery, and he was buried at the Troekurovsky cemetery in Moscow. In 2008, the head of Lukian's desert became Igumen Tikhon.

On May 29, 2011, celebrations were held to mark the 20th anniversary of the revival of the St. Lukian Desert and the St. Assumption Women's Monastery in Alexandrov. The monastery was awarded the medal of St. Blessed Prince Andrei Bogolyubsky of the first degree for diligent service.