In 1847, Bishop Jeremiah of the Caucasus ordered the establishment of a women's monastery with a church in the name of John the Baptist, three versts north of Stavropol. It was intended for widows and orphans of the clergy, as well as for the sick from other classes. The Stavropol community supported the initiative, helping both financially and in the construction of a two-story stone house behind the monastery fence, which housed a hospital. The land for the monastery was donated by the city's residents, including the Skomorokhov family.

In 1851, Bishop Joanniky of the Caucasus achieved a change in the community's status to that of a monastery. From 1852 to 1863, thanks to the efforts of Saint Ignatius, the monastery became a second-class monastery, and the abbess received the rank of igumenia. Saint Theophilact conducted the first monastic tonsure. The official date of the monastery's foundation is considered to be 1859. The first abbess, Seraphima, established rules according to the Athonite charter.

During the Russo-Turkish War of 1877-1878, the sisters prepared everything necessary for military hospitals and cared for the wounded.

By the early 20th century, the Ioanno-Mariinsky Monastery had become one of the largest in Southern Russia. It had five churches, buildings were constructed, a pond was improved, a garden was laid out, a free school for girls was opened, and art workshops were established. In the early 20th century, there were about 1,000 nuns and novices in the monastery.

In 1921, the monastery was closed. Its territory housed a colony for orphans, a rest home, and a branch of the regional psychiatric clinic. During the Soviet era, the buildings fell into disrepair. By the mid-2000s, four out of five churches had been demolished, and the fifth was rebuilt. After the collapse of the USSR, discussions about returning the monastery to the Church were not held for a long time.

In 2004, thanks to the support of the governor of Stavropol Krai A. Chernogorov and the chairman of the regional Duma Yu. Gontary, the transfer of the monastery to the Stavropol Diocese began. On December 24 of the same year, at a meeting of the Holy Synod of the Russian Orthodox Church, the opening of the Ioanno-Mariinsky Women's Monastery in Stavropol was blessed.

The nuns received part of one of the remaining buildings. A church in the name of the Venerable Seraphim of Sarov was arranged, and work began on the restoration of one of the churches. In the first year of the monastery's revival, the sisters organized free English language courses for children and began to assist the psychiatric clinic. In early 2006, an act was signed for the return of a number of premises of the monastery to the Stavropol Diocese.