With his future brother-in-law Vitaly Primakov Kotsiubynsky actively participated in the storming of the Winter Palace during the October Revolution.

Later, he headed the Red Guard detachment of Moscow-Narva Distinct (Saint-Petersburg) against the forces of Kerensky – Krasnov, being also the commandant of the district.

In January 1918 he became the Chief of Staff of the Soviet Ukrainian People's Republic and chairman of the military collegiate, nominally heading the army of the Petrograd Red Guards and Baltic Sailors in the fight against the national forces of the Ukrainian People's Republic which controlled Kyiv in February 1918.

In February 1935, he was arrested while being charged with anti-Soviet activities and convicted by the decision of the Special Board of NKVD to six years of exile in Almaty.

There, together with Vasyl Poraiko, Holubenko, Tytar, Tyrchuk, Volodymyr Lohinov and Pleskachevsky, he was charged with directing activities of a secret Trotskist center in Ukraine (Ukrainian Trotskyite Opposition) at the behest of Georgy Pyatakov.

There exists the Letter without envelope to Kotsiubynsky from Serhiy Okhrymenko in which the Ukrainian scientist blames him for bloody crimes against his own people.