213 years ago, far from large cities and noisy roads, the first Black Sea monastery was founded. Empress Catherine II, gifting lands to the Black Sea people, ordered the creation of a men's monastery named Ekaterino-Lebyazhskaya Nikolaevskaya Desert. The monastery was to follow the example of the strict life of the monks of the Sarov Monastery. The first abbot was the former hieromonk of the Samara Monastery, Theophan, who was elevated to the rank of archimandrite and arrived at the monastery in 1796. The desert arose in a barren place where there was nothing but reeds and untouched land.

The first buildings on the island were straw huts, where along with the abbot lived one hierodeacon, a hieromonk, and fifteen Cossack novices. Archimandrite Theophan, possessing experience and talent as a builder, diligently set about establishing the desert. He made contracts with merchants from Rostov and workers from all over the Black Sea region, traveling many miles in a carriage. He involved military elders in the construction, among whom were notable figures of the Black Sea region. The ataman Zakharij Chepiga donated a dam mill and a thousand rubles to the monastery.

Military judge Anton Golovaty and military scribe Timofey Kotlyarevsky, like many other elders, donated a thousand rubles each from their savings. The church buildings were constructed according to special drawings, although there was no overall plan. The first structures were made of logs, boards, and reeds, plastered with clay and thatched with reeds. Thus, the refectory church, cellar, kitchen, bakery, brotherhood quarters, hospital and abbot's cells, and stable appeared. To store monastery supplies, drinks, and food, a barn was built, cellars were dug, and an icehouse was created. The territory was enclosed with a fence made of pine boards. The construction was challenging, as building materials were delivered from Yeisk, Rostov, and other places in the Black Sea region.

Despite the difficulties, the monastery did not forget its main purpose, the observance of prayer rules according to the statutes of desert communal monasteries. This primarily concerned the divine services. The communal rule was observed, with evening prayers, vespers, midnight office, matins, and hours being held. On major holidays, all-night vigils were conducted with the reading of Sacred Scripture, and on lesser holidays, praises according to the statute. In their free time, the inhabitants read patristic literature and Sacred Scripture, delivered by Anton Golovaty along with the vestments from the abolished Kyiv-Mezhyhirsk Transfiguration Monastery.

The first inhabitants of the desert were Cossacks, wounded in war and exhausted by a hard nomadic life. They were elderly and crippled individuals who decided to spend their last years in the monastery. Their sincere desire was to die in the monastic order. A long period of obedience was mandatory for the dedication to monasticism, but many Cossacks died without undergoing it. Archimandrite Theophan, with the support of the military leadership, requested the Holy Synod to allow the tonsure of elderly Cossacks, and the Synod, as an exception, granted permission.

Residents of the village of Lebyazhiy Island, including Nina Maltseva, Tatyana Kirichenko, Galina Yeshchenko, and Raisa Maximova, began educational work to revive the history of the monastery. Kirichenko and Maximova led a school club, the materials of which formed the basis of the school local history museum. Thanks to the efforts of the workers of the poultry farm 'Lebyazhiy Island', a church parish was recreated in the Chepiginskaya stanitsa at the Holy Trinity Church.

Parishioners shared memories of Lebyazhiy Island in the 30s-40s of the 20th century, when evidence of the historical shrine of Kuban was found during the construction of the state farm: a partially destroyed bell tower and the burials of monks.

On July 4, 2011, the monastic brotherhood settled in the building of the former House of Culture of the Lebyazhye-Chepiginskoye JSC, marking the revival of the Ekaterino-Lebyazhskaya Nikolaevskaya Desert. Currently, a monastery church is being built in honor of Saint Nicholas.