In 1723, Metropolitan Joanniky established an archbishop school in Kolomna for the children of clergy and those preparing for the priesthood. The first 30 seminarians completed their two-year studies in 1725, and the next graduating class numbered 120. Until 1799, the future Metropolitan of Moscow and Kolomna, Filaret Drozdov, studied at this school, who was canonized by the Russian Orthodox Church in 1994.

In 1799, the Kolomna Diocese was abolished, and the seminary along with the bishop's see was transferred to Tula. In Kolomna, which became part of the Moscow Diocese, a two-year spiritual school was established on the basis of the seminary at the request of the local clergy. Boys from the clergy class aged 8-10 were admitted. In 1917, after the October Revolution, the Kolomna school was closed, and many church ministers suffered. Among the new martyrs and confessors were graduates of this school.

In 1990, with the blessing of Metropolitan Juvenaly of Krutitsy and Kolomna, the Moscow Diocesan Spiritual School opened at the Holy Trinity Novo-Golutvin Monastery, which later became the Kolomna Spiritual Seminary.

In 2007, at the initiative of Nikolai Tsvetkov, Chairman of the Board of Directors of FC 'URALSB', and his family, with the blessing of Metropolitan Juvenaly, construction of a new complex for the Kolomna seminary began through the Enlightenment Fund 'META'. On August 12, 2012, the consecration of the church in honor of the Three Hierarchs and the new complex of the seminary buildings took place, with a total area of 9,000 square meters.