During the Russian Civil War, Bogdanov joined the Red Army at Petrograd in June 1918. He was appointed a platoon commander in the 4th Kostroma Regiment, and from April 1919 commanded a company of the 2nd Reserve Regiment. From January 1920 he served as a company and battalion commander of the 502nd Rifle Regiment of the 56th Rifle Division, fighting in the Polish–Soviet War in battles in Vitebsk, Minsk, and Vilna Governorates. For his "exceptional courage in battle," Bogdanov was awarded the Order of the Red Banner. He returned to the 2nd Reserve Regiment to command a platoon in October 1920 and in January 1921 transferred to command a company at the 40th Kostroma Infantry Courses for Command Personnel. Between 10 May and 20 July, he participated in the suppression of the Tambov Rebellion as a company and battalion commander and acting chief of the course.