During the 1939 invasion of Poland, his apartment was destroyed and he moved to share an apartment with fellow chess player and his closest collaborator, Marian Wróbel. A Gestapo raid on the apartment in January 1940, during an informal meeting of Warsaw chess players, led to the arrest of all present. The non-Jewish participants were released a week later, Przepiórka and the other Jewish players (including Stanisław Kohn and Moishe Lowtzky and Przepiórka's son-in-law Jakub Rabinowicz) were subsequently executed by the Germans in Palmiry. The exact date of his death is unknown; it is presumed to be April 1940.