Prince Andrei was killed in his castle, and the site of his death under the stairs of the stair tower has been preserved to this day. Perhaps, in atonement for this crime, the monastery was founded in Bogolyubovo. Nikolai Voronin suggested that the monastery on the castle grounds appeared under Andrei's successors in the early 13th century; however, early information about the history of the monastery is scarce and refers to a later time. It is not mentioned in academic lists of ancient Russian monasteries.

According to the decree of Tsars Ivan and Peter Alexeyevich in 1687, the monastery became a patriarchal house monastery, in 1753 it became synodal, later it came under the management of Vladimir archbishops, and from 1882 until its closure, it was managed by the vicar bishops of the Vladimir diocese. When the states were established in 1763, the monastery was assigned a 3rd class, in 1872, a 2nd class, and in 1891, a 1st class. A huge cathedral in honor of the Bogolyubskaya Icon of the Mother of God was built from 1855 to 1866 in the 'Russian-Byzantine style' according to the design of Konstantin Ton.

In 1921 and 1923, the abbot was the vicar of the Vladimir diocese, Bishop Afanasy Sakharov of Kovrov. On June 3, 1923, the monastery was closed, and on September 17 of the same year, the presidium of the Vladimir district executive committee decided to transfer all the property of the former monastery to the district and volost executive committees. By the decree of December 21 and the Vladimir regional land management on January 8, 1924, the ensemble of the former monastery with its property was transferred to the museum department.

In 1991, part of the buildings was transferred to the monastics led by Schema-Hegumen Nikodim. On January 14, 1997, by the decision of the episcopate, 60 sisters from the Zadonsky Spaso-Transfiguration Monastery were transferred here, leading to the creation of two monasteries, one male and one female. The active revival of the monastery began: the cathedral of the Bogolyubskaya Icon of the Mother of God was completely plastered, steam heating was installed, chandeliers were set up, the central one weighing about 2 tons and nine small side ones. The floor was laid with granite and marble, white marble was used to decorate the solea, altar, throne, sacrificial table, and heavenly place. The frescoes were restored, and in 2002 a new three-tiered carved gilded iconostasis was made. Economic buildings were constructed, a fruit orchard was planted, and the cell buildings were restored. Sewing, icon painting, and carpentry workshops are in operation. The surroundings are filled with festive bells weighing 1050, 2500, and 8000 kg. A chapel and two baptistries, monastic and secular, were built at the holy spring by the walls of the monastery.

The tradition of the procession with the Bogolyubskaya Icon of the Mother of God, established in the 18th century in memory of the miraculous cessation of the plague through prayers before the icon, has been revived. The procession from Vladimir to the Holy Bogolyubsky Monastery is held annually on July 1, the day of the celebration of the Bogolyubskaya Icon of the Mother of God.

With the efforts of the Holy Bogolyubsky Monastery, the construction of a dependency in the Spas-Kupalishche area of the Sudogodsky district, located at the confluence of the Sudogda River into the Klyazma, has been completed. Since 2001, with the blessing of Archbishop Evlogy of Vladimir and Suzdal, a monastery complex with a cell building and economic structures has been erected on the empty site, a miraculous spring has been arranged, and the restoration of the Spaso-Transfiguration Church has been completed, where services have been resumed.