Mikhalkovo is first mentioned in the land registry book of 1584 as the property of Semyon Fomin, son of Tretyakov. The name is likely related to the nickname or surname of the first owner. By the mid-17th century, Mikhalkovo is already listed as the estate of I.I. Dashkov and remains in this princely family. Under the Dashkovs, a fruit orchard was planted, ponds were dug, and a wooden manor house was built, surrounded by peasant yards.

After her husband's death, the estate passed to E.R. Dashkova, who sold it to her guardian, Count N.I. Panin, before leaving for abroad. Panin himself did not live there, and the estate served as a summer residence for his brother, P.I. Panin. In 1778, English priest W. Cox described the estate as located four hours' ride from Moscow, surrounded by forest. The servants' quarters consisted of two rows of wooden buildings with beautiful facades, and the structures were designed in the style of English parks with ponds and meadows.

From 1780 to 1784, a stone estate was built under the guidance of P.Ya. Plyuskov. The central element became the parade courtyard with a fence and wings, adjacent to a linden park with ponds. The approach alley ended in a semicircular courtyard with a house, wings, and towers. Behind the house, a regular park began with a cascade of ponds and a gazebo-landing. After the death of P.I. Panin in 1789, the estate changed owners several times and in 1803 passed to industrialist D.E. Grachev. In the 1860s, V.I. Yokish bought Mikhalkovo, leaving Grachev only the main house, which was destroyed in the 1880s. Factory production negatively affected the estate: the wings were rebuilt, the towers were bricked up, the decorative wall was destroyed, and part of the territory was sold for summer cottages.

During the Great Patriotic War, the oak park and alleys were cut down for firewood. In the 1950s, the estate was restored, the parks were improved, and alleys were planted. During the restoration in 1994, lost elements were restored, and the regular park with a cascade of ponds was revived. Today, the estate retains the southeast parade gates, service building, southern gates with battlements in the shape of 'swallow tails', the southwest wing, which houses a hotel, part of the massive wall with buttresses, towers of the western gates, cascades of ponds, and gazebo-rotundas.