The monastery was founded by hieromonk Joseph, the former priest of Stepanshchevo village in Kozlov vicinity. In 1627, he settled in the woods on the bank of the Lesnoy Voronezh River. With time other monk life lovers started joining Joseph, so they created a small community. Soon they wanted to have their own church and in 1635-1636 they built a wooden church in the name of Holy Trinity with an altar of the Dormition of the Mother of God. Hence, the name of the monastery – Holy Trinity monastery. The first hegumen was assigned as the archbishop. That was Elder Joseph himself.
By the end of the 17th century, Kozlov monastery was known for its strict monastery rules and special spiritual organization. In many ways, this organization became possible thanks to hegumen Kirill (Baturin) running the monastery in the 70s of the 17th century. Hegumen Kirill started the construction of stone Dormition church consecrated on February, 9, 1672.
In 1683, Tambov bishop Pitirim gave Kozlov archimandrite a church-building charter for the building of stone Holy Trinity church. The construction started in 1683 and completed in 1687. St. Pitirim donated the icon of Holy Trinity to the newly-built church where it became one of the most important sacred objects of Holy Trinity monastery. At that time it was the largest monastery of the diocese, the centre of spiritual education, a representative of the historical past of Tambov land. Unfortunately, in 1697, there was a fire in the monastery. It destroyed all the wooden constructions and damaged both churches. Almost all buildings had been restored by 1706.
A number of new constructions were built in the fist half of the 19th century: a stone two-storey building in 1801, a stone one-storey house in 1816, a stone bell tower in 1818-1822. By the beginning of the 19th century the monastery had had a look that remained unchanged until its destruction during the Soviet years.
Like the majority of other monasteries in the country, Holy Trinity monastery was officially closed in 1918. In 1926, former monastery buildings were given to I.V. Michurin for the organization of the first nursery on its territory. Two upper levels of the bell tower were dismantled. The monastery cemetery was destroyed. Only a corner tower, a fragment of the wall, the Dormition church (it was occupied by the museum of the Central genetic laboratory) and ruins of the bell tower had remained from the monastery by the beginning of the 50s of the 20th century.In 1999, the building of the Dormition church was handed over to Tambov eparchy. The rebirth of the monastery began. In 2007, the Holy Synod blessed the opening of Kozlov Holy Trinity monastery in Michurinsk.