Borovsky monastery was founded by St. Paphnutius of Borovsk in 1444 on a beautiful high bank where the Istrema River flows into the Protva River. Upon the death of St. Paphnutius, his follower St. Joseph Volotsky became the hegumen of the monastery. Shortly after he introduced a strict monastic charter, which was rejected by the monks, he had to leave. He went to the principality of Volokolamsk, where founded a new cloister, later named the St. Joseph Volokolamsk Monastery. The Nativity Cathedral was built of a white stone on the site of an old wooden Nativity Church in 1467. In the XVI century the monastery was surrounded by stone walls and fortifications; the cloister turned into a strong fortress. At that time the stone refectory with a church devoted to Jesus Christ was built. In 1523 the belfry was built, which was replaced by the bell tower in 1688. In 1923, all the property of the monastery was transferred to the ownership of Glavmuzey, but soon after that it started serving as a prison, and after that as an agricultural college.

During the restoration of the 1960s some 194 blocks of white stone were extracted there. On 29 of them there were fragments of narrative and decorative paintings of the early XVI century. Before the church was returned to the Russian Orthodox Church, the monastery complex belonged to Borovsky Historical Museum.

The monastery was returned to the Orthodox Church and re-opened in March 1991. In the Nativity Cathedral there are relics of the founder of the monastery — St. Paphnutius of Borovsk.