Established by imperial decree on 9 November 1864, during the intensification of Russification in the former territories of the Polish–Lithuanian Commonwealth, it initially occupied the buildings of the former Order of the Visitation of Holy Mary on Ross' Street.

The Vilnius community consisted of nuns from the St. Alexis Convent in Moscow, who ran a school, an orphanage, as well as workshops for making liturgical vestments and writing icons at the monastery.

From then on, the monastic community resided in one of the wings of the complex of the Monastery of the Holy Spirit in Vilnius; the return to the original location took place in 2015.

[1] The establishment of the women's monastery in Vilnius was connected with the Russification campaign in the Lithuanian lands through the promotion of Russia's state religion – Eastern Orthodoxy.

According to the monastery's chronicle written in 1965 by Sister Barbara (Trofimowa), the Visitation nuns were allowed to leave the country along with most of the movable property.

[4] On October 22, Bishop Ignatius Żelezowski [pl] of Brest, in accordance with the resolution of the Most Holy Synod, bestowed upon her the dignity of hegumeness.

[4] In addition to the reconstruction of the main temple during the works, a second church was arranged, dedicated to the Protection of the Mother of God, and part of the residential buildings was adapted into accommodations for the orphanage.

[4] The hegumeness fully enforced the monastery rule's provisions upon the sisters (including those who came from Moscow), formed a choir from them, and herself engaged in the work of the orphanage from 1868 (i.e., from the admission of the first wards).

She received the title of hegumeness from Archbishop Macarius Bulgakov of the Russian Orthodox Diocese of Lithuania less than two months after formally assuming the position on 22 June 1878.

[4] Archbishop Juwenaliusz Połowcew [pl] of the Russian Orthodox Diocese of Lithuania appointed Hegumeness Moiseyeva (Lalina), who was brought from another monastery, as her successor.

[4] During the tenure of Hegumeness Moiseyeva, the nuns ran a school for 40 daughters of clergy or government officials working in the western and northern parts of the Russian Empire.

[4] According to a description in a Russian guidebook to Vilnius published in the early 20th century, the monastery was situated in an extremely picturesque location, and the complex of buildings occupied by the nuns was surrounded by a well-kept orchard.

[4] On July 22 (August 4 according to the Gregorian calendar) 1915, Metropolitan Tikhon of Moscow conducted the final Divine Liturgy in the monastery's Church of St. Mary Magdalene.

The nuns lost their landed estates granted to them before the war by the tsarist authorities, which were confiscated by Catholic institutions or Polish owners.

[4] Partly due to the circumstances of its establishment, the Polish authorities considered the Orthodox female monastery in Vilnius unnecessary and sought its liquidation.

As a result, the nuns were charged a high rent for the use of the buildings of the Monastery of the Holy Trinity, which was also nationalized after World War I, but leased to several Orthodox monastic communities.

The efforts of Hegumeness Nina to obtain permission to conduct fundraising for the construction of a new monastery from scratch, where the nuns could reside, also ended in failure.

[9]Ultimately, Hegumeness Nina obtained permission for the nuns to move to the buildings of the former parish school near another Orthodox church in Vilnius (St. Alexander Nevsky), located in the Naujininkai district.

[10] On 1 May 1937, the Synod of Bishops of the Polish Orthodox Church merged the two female monastic communities according to previous plans, and Metropolitan Dionizy obtained permission to build a larger residential facility for the 32 nuns of the monastery and to conduct fundraising for this purpose.

[11] At the time of the merger of the monasteries, the Synod of the Polish Orthodox Church considered naming the new community after the Holy Trinity; however, it was ultimately decided to adopt Mary Magdalene as its patron saint.

[6] As a result, in the early years after the war, the function of the church was fulfilled by a makeshift home chapel set up in the right wing of the building complex.

Four years later, with financial assistance from the Moscow Patriarchate, the monastery facilities were expanded: in addition to a two-story house for the nuns, a laundry room was built, the guardhouse was renovated, the complex of buildings was surrounded by a brick wall, and water and electricity were supplied.

[4] In 1989, the Council of Ministers of Lithuania declared the nullity of the decree abolishing the monastery, which gave it a legal basis for independent functioning also de jure.

[3] The Mother Superior of the Monastery of St. Mary Magdalene remained until 1968 Hegumeness Nina (Bataszowa), who then took the vows of the Great Schema with the name Barbara, thereby stepping down from her position (she died in 1969).

[19] In 2022, the construction of the branch church dedicated to the Icon of the Mother of God "Joy and Consolation" in Posakiszki (Bezdonys Eldership, Vilnius District Municipality) was completed.