With the outbreak of the 1948 Arab-Israeli War, he was trapped in Jerusalem. He died during the holiday of Shavuot of natural causes during the siege of the city by the Jordanian Arab Legion. As bodies could not be removed to the Mount of Olives during wartime, he was buried in the yeshiva courtyard on the condition that he would be reburied elsewhere after the war. However, his sons and successors, the Beis Yisrael and Lev Simcha, declined to go through with the reburial.