Illuste Manor was first mentioned in 1646, and it is known that in the Middle Ages, Illuste and its immediate surroundings belonged to the Holy Spirit Cistercian Nunnery in Lihula. The oldest records of the manor's buildings date back to the late 17th century. As shown in the 1685 manor reduction act compiled by the Swedish government, which detailed not only the general financial status of the manor but also thoroughly listed all the buildings belonging to the manor at that time, the Illuste manor ensemble of that era consisted of eight simple log buildings with thatched roofs. These included the main building, a granary, a horse stable, barns, and a threshing barn.
The parks of the two manors extended to meet each other, and in the western (seaside) part of the park was the family cemetery of the manor owners, the von Maydells. Illuste has also been referred to as the "Old Maid's Manor" because three sisters from the von Maydell family, all of whom were unmarried, lived there. In 1917, during a period of looting, the sisters, along with their brother Eduard Theodor von Maydell, the last owner of the manor, were executed. After the manor was expropriated, it served various functions: first as an economic center, then housed border guards, in 1939 Russian soldiers, later it was used as a summer camp for the Pioneers' House of the October District of Tallinn, then as a sports base. In recent decades, it hosted summer camps for the Tallinn Kristiine district's sports school.
As a result of the property reform, Illuste Manor became the property of the City of Tallinn and was managed by the Tallinn Sports and Youth Department. However, it was eventually deemed impractical to continue using the manor complex in its existing manner. In May 2013, the Tallinn City Property Department announced a public written auction, which was won by the non-profit organization Siili Palliklubi. Illuste Manor was separated as an independent economic unit from Siili Palliklubi, and in April 2014, a separate limited liability company, Illuste mõis OÜ, was established to manage, renovate, and develop the manor.