The five-domed stone church of the Epiphany was built in the 17th century. It is known that in 1757, along with the construction of the monastery fence, the entrance to the Epiphany church was "laid." In 1763, the church suffered from a fire, but not completely, as funds were only collected for the restoration of the iconostasis, which was updated in 1848 with the funds of the Ryazan merchant Fyodor Prokopyevich Filatov. In this church, as S.D. Yakhontov believed, Moscow architecture was preserved, and the bell tower had "ears." The refectory contained two chapels: the Protection of the Holy Virgin and Saint Evangelist John the Theologian. The first chapel was established in 1647 and consecrated on July 14 by the Most Reverend Moses. The floor in the Protection chapel was repaired, and the chapel itself was updated in 1848 with the funds of merchant I.V. Osminin. The second chapel was established in 1779 by State Councilor and Knight M.K. Vasilyev and consecrated by the Most Reverend Simon Lagov.

In 1855, the provincial architect Voronikhin was tasked with inspecting the new iconostasis in the chapel of the Apostle and Evangelist John the Theologian, created with the funds of court advisor Mrs. Pochtinova by Ryazan craftsman Vasily Lyubomirov. Voronikhin noted in his report that although the iconostasis was made with deviations from the plan approved by the Archbishop of Ryazan Gavriil Gorodkov, "the entire work and arrangement of the iconostasis fully achieves the splendor of the temple and its surroundings." In modern terms, the iconostasis was good, and the deviations were made at the request of the organizer. The only remark concerned the image of Mary Magdalene, which did not comply with church canons. By the 20th century, this chapel had not survived. In 1888, the Ryazan diocesan reports announced the consecration of the updated Epiphany church of the Spassky men's monastery, which took place on October 16. The Divine Liturgy was performed by the Most Reverend Feoktist, Archbishop of Ryazan and Zaraysk, and Theodosius, vicar Bishop of Mikhailovsk. The church is associated with a tent-shaped bell tower with six bells. Two of them had inscriptions. One stated that the bell was cast in 1647 during the reign of Tsar Alexei Mikhailovich and dedicated to the All-Merciful Savior. The second bell, cast in 1641, had an inscription about its donation by Elder Jonah, nicknamed Crane. These bells were removed after the 1917 revolution, as their ringing allegedly disturbed the working people. Few know that in the second half of the 17th century, there was a church over the gates in the name of Varlaam of Khutyn, consecrated on June 17, 1679 by the Metropolitan of Moscow Joseph. It existed for a short time, as in 1692, after the collapse of the Assumption Cathedral, the Varlaam church was also damaged and was not restored.

After the revolution, various organizations were located in the Epiphany church, and from the 1960s, the ZAGS archive was housed there. In 2007, the Spaso-Preobrazhensky Cathedral and the Epiphany church were returned to the monastery, but the archives left these premises only a year later. From 2008 to 2017, restoration work was carried out on the facades, drums, and domes.