During the May Coup d'État in Poland Filipkowski with an infantry regiment under his command supported the revolters of Piłsudski against the government. He remained in the military until the outbreak of World War II. He fought in the Polish Defensive War as a commander of an improvised infantry unit. Captured by the Soviets on 2 October 1939, he was imprisoned in Lwów. However, he managed to escape from the prison and moved to German-held General Government. There he hid in Otwock and then in Warsaw, under a variety of false identities. He joined the SZP resistance organization, which was later reformed into the Association of Armed Resistance and in the end into the Home Army. As one of the high-ranking Polish officers who knew the city of Lwów - yet were not known to a wider public prior to the outbreak of World War II, Filipkowski was a perfect candidate for a chief of Polish resistance in that town. In early 1940 he returned there under a false name and started to organize the Polish resistance. Initially under Soviet occupation, he continued his work as a Home Army inspector for the area of the city after the German take-over of the area in 1941. On 1 August 1943 he was made the commander of all Home Army units in the region.