The desert is located on the right bank of the Obesta River, not far from its confluence with the Kleven River, in a picturesque plain. The history of the monastery begins with the appearance of the miraculous icon of the Nativity of the Most Holy Theotokos in the first half of the 16th century. At that time, this territory was part of the Krupetskaya volost and was covered with dense forest, where beekeepers placed hives in the trees. The forest where the icon appeared was called "bortnoye ukhzhye."

The miraculous image of the Mother of God was found by beekeepers on one of the pines, shining with a wonderful light. From the root of the pine, where the icon was found, a spring of healing water flowed. Many people began to come to the place of the icon's appearance. One hermit, whose name is unknown, settled near the icon and built a chapel, with the participation of monks from the Molchensk Pechersk Desert, which is why the icon received the name "Desert-Glinskaya." After the chapel was completed, the icon was removed from the pine and placed in the church. However, the next day it was back on the pine. After the icon was removed again and returned to the pine, the abbot ordered the tree to be cut down. In the late 16th century, Fyodor Milonov and his companions built a wooden church here in honor of the Nativity of the Most Holy Theotokos.

The name "Glinskaya" has two explanations: some believe it is related to the clay extraction by potters, while others relate it to the family of the princes of Glin, who owned this area. It is most likely that the name is connected to the princes of Glin, descendants of Khan Mamai.

The Glinskaya Desert is closely associated with the Putivl Molchensk Monastery, founded by monks from the Molchensk Desert. In the late 16th century, after Tatar raids, the construction of the Putivl Monastery began. In 1605, after the devastation of the Molchensk Desert by the Poles, the monks relocated to Putivl. From the early 16th century until 1648, the Glinskaya Desert accumulated rich spiritual experience. From 1643, the Putivl monks owned the lands of the Glinskaya Desert, but for a long time did not hold services. In the early 18th century, the monastery strengthened its material position, owned many lands, and had a rich economy. In May 1781, a two-story stone church was consecrated.

In the church and its chapels, there were wooden, carved, and gilded iconostases, decorated with silver vestments and crowns. In the late 18th and early 19th centuries, the cathedral church and bell tower were covered with black iron. The Glinskaya Desert owned forests where bears, wolves, and other animals lived. On the arable lands, rye, oats, and buckwheat were sown. Peasants engaged in agriculture, while women spun and wove. Near the Desert, a pond with a mill was arranged, as well as an apiary for collecting honey and wax. From 1764 to 1785, the monks improved the monastery by building a stone church and a fence.

In the early 19th century, the Glinskaya Desert became a spiritual hospital, where errant clergy were sent. Abbot Philaret Danilevsky, who served from 1817 to 1841, transformed the monastery by introducing a strict communal rule. He also built facilities for workshops and hotels.

In 1860, the chapel of the Near Skete was transformed into a church, and in 1864, the reconstruction of the cathedral church was completed. In 1874, a hospital building for pilgrims and monks was constructed. The Glinskaya Desert actively supported popular education and published spiritual literature. In the early 20th century, the monastery received up to 60,000 pilgrims annually, providing them with housing and assistance.

With the advent of Soviet power, the monastery was closed, and its property was looted. In 1922, part of the land and the mill were confiscated, and in September of the same year, the Desert was closed. A children's town was created in its place. In 1942, the monastery was reopened, but only a few buildings remained. In 1947, a plot of land was allocated to the monastery, where they began to sow grains and grow vegetables.

On July 13, 1961, the Glinskaya Desert was closed, and its property was transferred to a nursing home. In 1994, the monastery was revived, and in 1996, it was granted Stavropigia.