Kostrzewski became professor of prehistory at the newly founded university of Poznań in 1919, and from 1934 conducted the excavation of the Iron age settlement of Biskupin, which he continued after the war. After 1918, Kostrzewski became involved in bitter polemics about the ethnic ascription of the Lusatian and Pommeranian culture with the chauvinist German archaeologist Bölko von Richthofen, later an important supporter of the leading Nazi archaeologist Hans Reinerth.

After the German occupation, Polish universities and museums were closed, the finds often transported to Germany, and many scholars arrested, tortured and detained or murdered. Kostrzewski had to hide from the Gestapo during the whole war, but returned to his Poznań chair in 1945.

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