After the German occupation and the establishment of the Protectorate of Bohemia and Moravia he became a member of a secret underground organization "Obrana národa" ("National Defense"). It is supposed that at the same time he established connection with Soviet intelligence. In June 1939 he fled to Poland, and as the oldest and most senior officer formed Czechoslovak military unit in Kraków. This unit, under the name Legion of Czechs and Slovaks, took a limited part in the war after the German invasion of Poland. After the Polish defeat he diverted a group of about 700 officers and men to the Soviet Union. They were interned gradually at several places for almost two years, until the German attack on the Soviet Union. Meantime Svoboda successfully negotiated with the Soviet government the transfer of Czechoslovak soldiers to France, and after its fall to Great Britain (twelve transports: 662 men, 12 women, 6 children). At that time the Czechoslovak government in exile was not officially recognized either by France or by Great Britain. After the outbreak of the German offensive against the Soviet Union, Svoboda became head of the Czechoslovak military units on the Eastern Front. The Czechoslovak units fought the Germans for the first time in March 1943 at the Battle of Sokolovo in Ukraine.