Kotovsky was born in the Bessarabia Governorate, the son of a mechanical engineer. Officially, Kotovsky claimed to be born in 1887. He also had five siblings. His father was a Russian citizen of Polish descent and his mother an ethnic Russian. By ancestry, Kotovsky hailed from an aristocratic Polish family from Kamyanets-Podilsky. His grandfather, because of connections with members of the Polish uprising, was dismissed from Russian service and eventually went bankrupt. His father was forced to move to Bessarabia and become a Russian burgess. Kotovsky suffered from a marked stuttering and was left-handed. At the age of 2, he lost his mother and, at 16, his father. Kotovsky was raised by his godmother, Sophia Challe, the daughter of a Belgian engineer and friend of Kotovsky's father, and a godfather, the landowner Manuk-bey. Manuk-bey aided and supported Kotovsky's enrollment and stay at the Cucuruzeni Agricultural College. He intended eventually to send his godson to Germany for advanced agricultural courses, but his dreams were cut short by his death in 1902. While studying at the agricultural college, Kotovsky became involved with the local political club of Socialist Revolutionaries. After graduation in 1900 he began work as an assistant to an estate manager, but not for long. Kotovsky was fired for various acts of theft, fraternization, and other misdeeds. With the start of the Russo-Japanese War, he failed to report to his military draft processing station. In 1905, he was arrested for evasion of military service and sent to the 19th Kostroma Infantry Regiment, headquartered in Zhytomyr. He soon deserted from the military and organized his own criminal gang, conducting raids, setting estates on fire, robbing, and terrorizing the local population. On January 18, 1906 Kotovsky was finally arrested, but managed to escape after six months in the Chisinau prison. On September 24, 1906, he was again arrested again and sentenced to 12 years of katorga. Kotovsky began serving his sentence at Nerchinsk katorga until 1911. He later spent more time in various prisons across the Russian Empire:. At katorga, Kotovsky cooperated with prison authorities and was put in charge of a 10-man team of construction workers who were building a railroad. In 1913 he became a candidate for the amnesty commemorating the 300th anniversary of the Romanov dynasty. However, it was decided not to release bandits on the day of the amnesty, and on February 27, 1913, Kotovsky managed to escape from katorga and return home to Bessarabia. At first he lived in secrecy, working as a loader and worker doing unskilled, heavy jobs. He then became the leader of a local criminal gang of raiders. One of his most notorious feats was the successful theft of the State Treasury office in Bender, Moldova. On June 25, 1916 Kotovsky was unable to escape from police after another raid. He was surrounded by a squad of secret police and, after being wounded in the chest, he was arrested. The Odessa Military District court sentenced him to capital punishment and death by hanging. On death row, Kotovsky wrote letters of repentance and begged to be sent to the front lines. Upon the abdication of Nicholas II, a riot took place at Odessa prison after which the prison became self-governed by inmates; the Russian Provisional Government announced a wide political amnesty for all prisoners to be released.
Kotovsky appears as an important character in the novel "Chapayev and Void" by modern Russian writer Viktor Pelevin. In this novel, Kotovsky is shown as a man who talks about philosophical questions and is addicted to cocaine.
