Soon after occupation he organized a partisan unit at Świętokrzyskie Mountains, however, after this unit was defeated by the Germans, he went to Warsaw by late October, joining the first Polish resistance organization, the Service for Poland's Victory. In November, he was assigned to Vilnius, which was at the time occupied by the Soviet Union according to the Molotov–Ribbentrop Pact. The SZP was transformed into Związek Walki Zbrojnej. When in April 1941 Soviet NKVD arrested the commander of the ZWP in the Vilnius region, general Nikodem Sulik, Krzyżanowski "de facto" replaced him, with his position being officially confirmed by general Stefan Rowecki in August. In 1942 ZWP was transformed into Armia Krajowa (AK).