Since its beginning in 1921, Estonia's diplomatic mission in Moscow has operated in the same building.

The Estonian Embassy is located in the heart of historic Moscow, sandwiched between Maly Kislovsky Pereulok and Kalashny Pereulok. The Kremlin, the Arbat and the Moscow Conservatory are all right nearby.

The building itself, an early art nouveau-style urban manor designed by architect Alexey Shcheglov, was built in 1903. A modern addition was built in the 1980s and used as a guesthouse; this part has since been converted to living quarters for embassy employees as well as the consulate.

From 2014-2019, the Ministry of Foreign Affairs in cooperation with state real estate company Riigi Kinnisvara AS (RKAS) and Inseneribüroo Telora carried out extensive reconstruction work at the embassy building. The building's primary design work was provided by Innopolis Insenerid, with KAOS Arhitektid (Toomas Adrikorn, Margit Argus, Margit Aule, Kaiko Kerdmann) responsible for the architectural and interior architectural design.

Reconstruction and renovation work began in autumn 2016, beginning in the embassy's newer half. Work on the historic half began in 2018 and was completed in January 2019.

In the course of renovations, historic furniture and artwork were also restored by a team from the Conservation and Digitalisation Centre Kanut of the Estonian Open Air Museum, led by Viljar Vissel, and in collaboration with Alar Nurkse, a painting conservator of the Art Museum of Estonia.

Following an art competition arranged by the Ministry of Foreign Affairs, the renovated embassy building will also display prime examples of modern Estonian art.