The first mention of the monastery in chronicles dates back to 1620, when it was founded by monk Gelasius. The monks lived and prayed in chalk caves, which in architecture and layout resembled the Kyiv-Pechersk Lavra, and were carved into one of the hills near the village of Chernyanka. In these caves were ascetic cells with a bed and table carved from chalk, as well as an underground temple.

The monastery existed for 144 years and was closed in 1764 by order of Empress Catherine II. The entrance to the caves was blocked, and services in the underground temple ceased. The Transfiguration Church of the monastery, built in the 1650s, became a parish church.

Over time, the residents of the village of Holki could no longer indicate the location of the gate chapel built in 1757, and the entrance to the underground monastery was lost.

In the mid-1970s, historians and local historians became interested in the caves, and the administration of the Chernyansky district decided to restore them. Partially restored Holkov caves were opened to visitors in the early 1990s, and restoration work continued.

In 1995, services began to be held in the underground Holy Trinity temple by clergymen of the Chernyansky district. Holki began to be visited not only by tourists but also by pilgrims.

In 1996, on the territory of the ancient Holkov monastery, three foundation stones were consecrated by Bishop Ioann of Belgorod and Stary Oskol for the construction of two churches and a chapel.

First, a gate church in honor of the Venerable Anthony and Theodosius of the Kyiv-Pechersk was built at the entrance to the caves, followed by the Vladimir chapel.

In December 1999, Archbishop Ioann of Belgorod and Stary Oskol consecrated the monastery church in honor of the Don Icon of the Mother of God. At a meeting of the Holy Synod of the Russian Orthodox Church on December 28, 1999, the opening of the Holy Trinity Holkov Men's Monastery was blessed.