In the second half of the 18th century, the estate was owned by the nephew of Peter I's associate, Savva Raguzinsky-Vladislavich, Count Yefim Ivanovich Vladislavich. According to legend, there was previously a metropolitan courtyard here, although no documentary evidence has yet been found. Already in the 17th century, stone chambers were built on this site, partially preserved in the foundation of the modern building, where ancient vaults can be seen in the basement. The main house, whose facade faced the now-lost Peterverigskaya Church, was erected at the turn of the 17th and 18th centuries.

In 1803, the estate was acquired by the director of Moscow University, Ivan Petrovich Turgenev, who lived here until his death in 1807. During this period, the estate became one of the literary salons of Moscow, frequented by N.M. Karamzin, M.M. Kheraskov, and V.A. Zhukovsky, with whom Turgenev's son, Andrei, was friends.

During the fire of 1812, the estate was damaged by flames. Only two decades later, it was purchased by merchant Pyotr Kononovich Botkin, who rebuilt the main house, giving the facades a late Empire style with Ionic capitals, garlands with ribbons, and rich stucco decorations on classical themes between the pilasters of the portico. At that time, two paired courtyard wings were also built.

Like during Turgenev's time, the Botkin house became a center of cultural and social life. Notable visitors included A.I. Herzen, N.P. Ogarev, V.G. Belinsky, I.I. Panayev, N.V. Gogol, L.N. Tolstoy, as well as actors M.S. Shchepkin and P.S. Mochalov. For some time, V.G. Belinsky lived here, befriending Vasily Botkin, the owner's son. The poet A.A. Fet, married to Maria Petrovna Botkina, often visited here as a relative. In the right annex to the main house, the famous Russian physicist Pyotr Nikolaevich Lebedev was born in 1866, whose father worked for the Botkin firm and rented an apartment here.

Pyotr Kononovich's granddaughter, Vera Petrovna, married Moscow mayor Nikolai Ivanovich Guchkov, brother of the well-known politician Alexander Ivanovich Guchkov. In 1907, Guchkov became the owner of the Botkin mansion while being the director of the tea trading company 'Petra Botkina Sons'.

In 1918, the estate was nationalized, and two years later, Guchkov emigrated to France. By that time, Vera Petrovna had already passed away in 1916.

In the early years of Soviet power, communal apartments appeared in the house, and in 1935, part of the estate was built over. After the war, it housed a kindergarten, nursery, storage for the 'Medicine' publishing house, and other state institutions. In the 1970s, the Moscow City Council for Tourism and Excursions (MGTES) was located in the estate. Currently, the building houses the Russian Military Historical Society (RVIO).

Restoration work at the estate was carried out in 2015-2016. In 2017, the Botkin estate was awarded a prize in the Moscow Government's 'Moscow Restoration' competition in the categories of 'Best Restoration/Adaptation Project' and 'Best Organization of Repair and Restoration Work'.