In 1917, Isakov moved to Petrograd and entered the Naval Guards School of the Imperial Russian Navy and graduated as a midshipman in March of that year. He briefly saw action against the Germans in West Estonian archipelago (Moonsund archipelago). He continued his service after the October Revolution in the Baltic Sea fleet as a torpedo officer, where he served on several warships, including the "Izyaslav", the "Riga", the "Kobchik" and the "Korshun". In 1918, he took part in several battles against the German Imperial Navy until the signing of the Treaty of Brest-Litovsk, which effectively ended the war between Russia and Germany, granting the Baltic Sea to the latter. In March 1918, Isakov participated in the Ice Cruise of the Baltic Fleet from the naval base at Helsingfors where Russian warships and icebreakers were transferred from the Baltic to the naval base in Kronshtadt near Petrograd. An authoritative Russian Navy source notes that Isakov completed additional courses in mine-sweeping and mine-laying in 1919 and then served in the Caspian Sea, returning to the Baltic in 1920 and subsequently serving in the Black Sea until the mid-1920s.