The monastery was founded in 1389 by the Bishop of Rostov, Saint Jacob. After being expelled from the city, he settled south of Rostov, near the Church of Archangel Michael, and built a wooden church in honor of the Conception of the Most Holy Theotokos. Soon, a small community gathered around the church, marking the beginning of a new monastery.

After the death of Saint Jacob, he was venerated as a saint, and his grave became a shrine. In 1549, he was canonized at the Makaryev Council. The relics of Saint Jacob rest in the Church of the Conception of Saint Anna.

The monastery, known as the Conception or Yakovlevsky Monastery, consisted of wooden structures until the end of the 17th century. The first stone building was the Trinity, later Conception Cathedral, erected on the site of the wooden church. The five-domed cathedral with three apses was consecrated by Metropolitan Jonah Sysoevich and painted by Yaroslavl masters in 1689. A stone canopy was built over the grave of Saint Jacob.

In the early 18th century, the monastery was under the patronage of Metropolitan Dmitry of Rostov. In 1702, he arrived in Rostov at the behest of Peter I and was ceremoniously welcomed at the monastery, where he held a prayer service. Dmitry of Rostov was buried in the Trinity Church, and a wooden tomb was erected over his grave. Two icons of the Mother of God were received by the monastery according to his will. In 1725, a northern Conception chapel was added to the cathedral, which later became a separate church. In 1754, the cathedral was renamed the Conception Cathedral, and the chapel was named in honor of Jacob of Rostov. In 1757, the canonization of Saint Dmitry of Rostov took place, leading to an increase in the number of pilgrims. That same year, a guesthouse for pilgrims was built. Metropolitan Arseniy commissioned records of miraculous healings at the saint's tomb, which are now kept in the archive of the Rostov Museum.

Since 1764, the monastery became stavropegial, subordinate to the Holy Synod. In the same year, it was assigned the buildings of the abolished Spaso-Pesetsky Monastery, including the Spaso-Transfiguration Cathedral of the 17th century. In 1765 and 1836, the monastery was referred to as the Spaso-Yakovlevsky Conception Monastery.

In the 1760s, a wooden carved iconostasis was installed in the Conception Cathedral, for which the Kharkov icon painter Veder wrote icons. By the end of the 18th century, the wooden walls of the monastery were replaced with a stone fence with towers and a bell tower. Brotherly cells and an abbot's house were built.

By the end of the 18th century, the art of cloisonné enamel icons flourished in the monastery. Metropolitan Arseniy invited icon painters to renew and create new icons. The Spaso-Yakovlevsky Monastery became the main customer for cloisonné icons. In 1794 and 1802, the Dmitrievsky Cathedral was built with funds from Count Nikolai Sheremetev. However, the relics of Saint Dmitry were not transferred to the new church. Sheremetev became the largest benefactor of the monastery, donating vestments and church utensils. In his memory, the Dmitrievsky Cathedral is called Sheremetevsky.

In the early 19th century, Elder Amphilochius, who was venerated after his death, labored in the monastery. In 1836, a church dedicated to Saint Jacob of Rostov was built on the site of the old chapel. That same year, a porch was erected at the Conception Cathedral, where tombs were installed.

In the 1860s, the iconostasis of the Dmitrievsky Cathedral was renewed. In 1836, the monastery received a new name, Spaso-Yakovlevsky Dmitriev Monastery.

The monastery was visited by many Russian emperors. In the early 20th century, new churches were consecrated. In 1912, a cave church was opened in the Yakovlev Church, and in 1916, a chapel in honor of the Vatopedi Icon. In 1909, a church in honor of the Tolga Icon was opened in the southwest tower.

Since 1909, Bishop Joseph was the abbot of the monastery. After 1917, services were held only in the Yakovlev Church. In 1923, the monastery was closed, and the buildings were used for residential purposes and workshops. Some property was transferred to a museum, while some was looted.

In the 1980s, the 18th-century iconostasis was dismantled. In 1991, the monastery was returned to the Russian Orthodox Church and renewed. The relics of Saints Abraham and Dmitry rest here, and the Vatopedi Icon is also kept. In 1996, a chapel was built over the spring in honor of Saint Jacob.