In 1920, Isakov was transferred and assigned to the destroyer "Deyatelni", which patrolled from the Volga River down to the Caspian Sea and later shelled the positions of Allied interventionist forces in the midst of the Russian Civil War. Noted for his distinction during the battles, he was made the gun battery commander of the destroyer "Izyaslav" in 1921. From 1922 to 1927, he served as a "shtab operative", or member of the deputy chief of staff, of naval forces in the Black Sea Fleet. In 1928, Isakov completed academic courses at the Naval Academy in Leningrad and from 1930, he was Chief of Staff of the Baltic Fleet. In 1932, Isakov became the professor and head of the naval art department of the Soviet Naval Military Academy and taught as a professor for five years until he was promoted commander of the Baltic Fleet. From 1938 to 1939, he headed the Naval Academy. Isakov was appointed vice-commissar of naval affairs, and in 1939, he led a naval delegation to the United States with the goal of purchasing new warships. He met with the Secretary of the Navy, but the delegation left empty-handed since the US was unwilling to extend aid to the Soviet Union. Isakov broke away from teaching with the onset of the Winter War and entered active service; he coordinated not only the movement of naval warships in the Baltic Sea but also the ground forces of the Red Army in the Soviet war against Finland. From 1941 to 1943 Isakov was the chief of the Main Maritime Staff. In 1946 to 1947, he was chief of the Main Navy Staff. In 1947 to 1950, he was deputy commander-in-chief of the navy. In 1950 to 1956, he was deputy Naval Minister. From 1957, he was a member of the Defense Ministry General Inspectorate.