The very first written reference to Kondopoga dates back to 1563. It became important after rich marble deposits were discovered nearby in 1757 and the quarries were founded. Kondopoga became a logistics hub for marble shipping to St. Petersburg. Later, iron ore deposits were found in the vicinity, which were shipped to metallurgical factories in Petrozavodsk and in Kentjärvi. By 1892, Kondopoga had forty-eight buildings, three hundred inhabitants, two churches, and a college and held an annual trade fair on September 8–15. During World War I, the Main Artillery Administrative Department of the Russian Military Ministry started construction of a nitric acid plant there, which was essential for gunpowder production. A hydroelectric power station was designed to meet considerable demand in the energy for such a plant. Kondopoga was well suitable for such a station due to significant water level drop between Lakes Nigozero and Onega. A 30 MW station was to become the largest in Russia. However, the October Revolution and the subsequent Civil War delayed the project, which was only revived in the Soviet time as a part of the GOELRO plan. According to the project, the waters of the Suna River were to be redirected towards the hydroelectric power station via the lake system. On July 19, 1923, Sovnarkhoz of Karelia ratified the formation of a building society to build a hydroelectric power station and a major pulp and paper mill. Kondopoga became the administrative center of a district in 1932 and was granted town status in 1938. At the time, its population was about fourteen thousand inhabitants. On November 3, 1941, during World War II, Kondopoga was occupied by Finnish troops and totally destroyed. Industrial plants and factories were looted, including the pulp and paper mill, hydroelectric station, granite and brick factories, furniture factory, and other facilities. Approximately 250 houses and apartment buildings were demolished along with concert halls, museums, kindergarten, school, hotels, fire station, and government offices. All bridges in the vicinity were blown up. The town was liberated on June 28, 1944 by Red Army's Karelian Front as part of Svir–Petrozavodsk Offensive. After the war, the town was rebuilt. In 1957, Kondopoga was declared the All-Union Komsomol building site. A number of new factories were built and the pulp and paper mill was also expanded. The population grew to 38,000 people. On the night of August 29–30, 2006, two ethnic Russians were killed and several others badly injured by Chechens, starting 2006 ethnic tensions in Kondopoga.
First recorded as early as 1495, Kondopoga retained a rare monument of Russian wooden architecture — the Dormition Church, built in 1774. The central column of this church was crowned by a hipped roof, 42 m in total height. The column was based on a central rectangular framework, with adjacent frameworks for the refectory and altar. The altar framework was covered by a traditional wooden roof, called a barrel roof. The church was burnt up in 2018 by a mentally disordered teenager, only few charred remains left at its place.
