Sofroniev Desert was founded in the late 19th century by Archimandrite Sophrony, when he was the abbot of the Arzamas High Mountain Desert. It was located in one of the forest areas belonging to the monastery. Archive records of the High Mountain Desert from 1891 mention that the monastery had two forest plots: the Abramov Dacha 6 versts away and the Nikolskaya 35 versts from the Desert. In other documents, they are referred to as the 'near' and 'far' forest. In the 'far' forest, the elder built a small house. By the decree of the Spiritual Consistory on November 16, 1907, Archimandrite Sophrony retired from the position of abbot and settled in the forest at the beginning of 1908. Four novices settled nearby, and a building with a chapel was constructed, where 12 girls lived, mostly daughters of his spiritual children, who later took monastic vows. On July 26, 1908, a church in honor of our Lord Jesus Christ was consecrated in the Desert.

By 2000, the women's skete of the Valaam Monastery had become a men's skete, and the female community was offered to find a new place. After searching, it was decided to settle in Sofroniev Desert, where only a few guards lived at that time. A year after the move, the community faced a trial: due to faulty chimney pipes, a fire broke out, destroying the prayer house used as a church. Only the Holy Gifts, liturgical vessels, and the locally revered icon 'Heal My Sorrows' were saved. With the appointment of Bishop Georgy, the community received a blessing for temporary, and then permanent residence. The monastery was issued an Antimension for the Divine Liturgy, which began in the chapel arranged in the sisters' building. During the week of the Triumph of Orthodoxy in Great Lent 2003, Bishop Georgy visited the monastery with the clergy of the Nizhny Novgorod diocese, the mayor, and representatives of the city Duma of Arzamas. Bishop Georgy performed a Litia at the grave of Archimandrite Sophrony, and soon a new church of the monastery was laid.

Today, monastic life has been revived in the desert. Through the efforts of the sisters and the prayers of Elder Sophrony, the monastery has transformed: under conditions of poor roads, lack of electricity, and insufficient funds, a new church of the Iveron Icon of the Mother of God, a burial church above the elder's grave, a chapel of the Kazan Icon of the Mother of God in the cells building, a new cells building, and economic structures have been built. In the village of Kovaksa, a dependency of Sofroniev Desert has been established.