There is a legend that Ilyinsky Pogost arose on the site of an ancient pagan shrine, where local tribes conducted sacrifices before the arrival of the Novgorodians. However, it is more likely that the pogost was founded in the 16th century by monks heading to Solovki. The first mentions of it appear in the "Charter of Privileges" of Novgorod Metropolitan Varlaam, issued to the Vodlozers in 1592.

Ilyinsky Pogost is adorned with the wooden church of the Prophet Elijah, built in 1798 on the site of an old tent-like church by local carpenters funded by parishioners. The construction was based on a project developed by professional architects and approved by the Olonets Consistory. The spiritual authorities did not allow the new church to be built in the old style, ordering the old one to be dismantled and a new one to be laid "in accordance with the plan." According to architect A.V. Opolovnikov, who first surveyed and measured the church in 1947, it was built at different times. The oldest part is the square base, to which the refectory and bell tower were later added. Initially, the bell tower was topped with a tent that soared upwards.

At the turn of the 19th-20th centuries, the monument was renovated: the bell tower lost its tent, which was replaced by a flattened "semi-dome" with a spire, and was sheathed with planks. The sheathing of the church and refectory combined all elements of the building into a single mass; the covered hanging passage between the bell tower and the vestibule, as well as two porches, disappeared. The interior also changed: the old iconostasis was replaced with a new one, "composed according to the rules of architecture." The new iconostasis, approved by the Olonets Construction and Road Commission, became a typical eclectic work of the second half of the 19th century. The ceilings and walls of the church were sheathed with boards.

Another feature of Ilyinsky Pogost is the log fence, reinforced with logs and covered with a gable roof. Such fences, giving structures the appearance of an ancient fortress, used to surround many monasteries and pogosts. This fence served as a model for the fence of Kizhi Pogost. There were shops in the fence where peasants and merchants traded during holidays and fairs. Trade was likely profitable, as extensive warehouses for merchant goods were set up on the neighboring island of Kolgostrov.

In the 1930s, Ilyinsky Pogost became deserted, losing priests and parishioners who were sent to camps.

In 1991, the revival of the monastery began. Since 2003, services have resumed at Ilyinsky Pogost. In 2004, Oleg Chervyakov, the director of Vodlozersky National Park, was ordained as a priest and became the rector of the Church of Elijah.

On December 23, 2006, by decision of the Holy Synod of the Russian Orthodox Church, the male monastery of the Holy Ilyinsky Vodlozersky Monastery was established at Ilyinsky Pogost. The newly formed monastery is served by Abbot Cyprian Grishchenko, hieromonk, hierodeacon, monk, and novices.