The Church of the Exaltation of the Holy Cross was built at the Pyatnitsky Gates, on one of the oldest sites of the Kolomna Kremlin. In the 15th century, there was a wooden church here with an altar in honor of the martyrs Flora and Laurus.

In 1764, a stone two-tiered church with a bell tower was erected on the site of the wooden church. The initiator of the construction was the Kolomna bishop Gabriel Kremenetsky. The upper church housed the altar of Saint Nicholas, which was moved from the abolished Church of Nicholas of Zaraysk from 1513. Along with it, an image, a copy of the Zaraysk icon created in the same year, was also transferred here.

In the late 18th century, the Exaltation Church was renovated with funds from the Kolomna merchant I.T. Meshchaninov. From 1790 to 1825, the revered Don Icon of the Mother of God from the 16th-century Pyatnitsky Gates temporarily resided here. In 1832 and 1837, the church underwent radical reconstruction funded by the Sharapov sisters.

The church did not have its own parish and was attached to the Assumption Cathedral, where services were conducted by cathedral clergy. In the 1920s, a parish was formed here, served by monks expelled from the Trinity Novo-Golutvin Monastery. The Exaltation Church was the last to be closed in the Kremlin. In the 1930s, the monks were arrested, and their fates remain unknown.

The building housed a workshop for disabled individuals, and almost all church items were lost. The domes and the bell tier were destroyed. In the 1980s, the premises were used as a workshop and storage for the Kolomna Local History Museum.

In 1994, the church was returned to the Orthodox community. A new two-tiered iconostasis was created, and ancient icons were transferred to the church. Many professional artists are nurtured in the community, and pilgrimage activities are actively developing.