More than six centuries ago, in the 1350s, the venerable Stefan, a native of the Kiev-Pechersk Monastery, founded the holy abode. Due to the oppression of the Uniates that spread in the Kiev principality after its conquest by the great Lithuanian prince Gediminas, Stefan was forced to leave his homeland and go to Moscow. There, he was warmly welcomed by Grand Duke Ivan II Ioannovich the Quiet, who offered him to settle in any Moscow monastery. However, Stefan sought solitude and chose a quiet place in the northern part of the Moscow principality, in a forest area on the Makhriщ River, 35 kilometers from the abode of Sergius of Radonezh. The Grand Duke granted him a charter for the use of this land and donations for the construction of the monastery. News of Stefan's piety quickly spread, and those wishing to dedicate themselves to monastic life began to flock to him. Soon, the need arose to build the first church, refectory, cells, and enclosure. All of this was successfully erected, and Stefan went to Moscow for the blessing of Metropolitan Alexius for the consecration of the church in honor of the Holy Life-Giving Trinity. Alexius ordained him as a presbyter and appointed him as the abbot of the monastery. In the Makhriщsky Monastery, as in the abode of Sergius, a communal rule was introduced.

After the Time of Troubles, the revival of the Stepan-Makhriщsky Monastery is associated with Metropolitan Platon, an outstanding theologian and preacher, who did much for the transformation of spiritual schools and the Moscow Spiritual Academy. Platon loved the monastery and spent summer weeks there. Thanks to his care, a stone enclosure, churches of Venerable Sergius of Radonezh and the Holy Apostles Peter and Paul, brotherhood buildings were constructed, and the ancient Trinity church was rebuilt. In the 19th century, the monastery continued to develop: new buildings were constructed, a three-tiered bell tower was added to the Trinity church, and stables and a greenhouse were built. In 1900, hieromonk Alipiy organized an orphanage for orphans and poor children in the monastery, as well as a church-parish school. The monastery had a large library, which was replenished with periodicals.

However, all this beauty soon faced trials. In 1922, the monastery was closed, and its buildings were handed over to various organizations. In 1942, the Stefan and Trinity churches were dismantled, and their rubble was used for the construction of an airfield. The monastery gradually fell into disrepair and decay. In 1993, Bishop Evlogiy of Vladimir and Suzdal erected a memorial cross in honor of the 600th anniversary of the death of Sergius of Radonezh. The first inhabitants settled in the ruined building, led by nun Elisaveta, who became the abbess. The Makhriщsky Monastery became a skete of the Alexandrovsk Uspensky Women's Monastery, and in 1995 it gained independence. Overcoming many difficulties, the abode was revived, and services began in the church of the Holy Apostles Peter and Paul. God's blessing manifested in the myrrh-streaming icon of Venerable Seraphim of Sarov.