At the end of July 1941, three prisoners disappeared from the camp, prompting SS-Hauptsturmführer Karl Fritzsch, the deputy camp commander, to pick 10 men to be starved to death in an underground bunker in order to deter further escape attempts. When one of the selected men, Franciszek Gajowniczek, cried out, "My wife! My children!", Kolbe volunteered to take his place.

In his prison cell, Kolbe celebrated Mass each day and sang hymns with the prisoners. He led the other condemned men in song and prayer and encouraged them by telling them they would soon be with Mary in Heaven. Each time the guards checked on him, he was standing or kneeling in the middle of the cell and looking calmly at those who entered. After two weeks of dehydration and starvation, only Kolbe remained alive. The guards wanted the bunker emptied and they gave Kolbe a lethal injection of carbolic acid. Some who were present at the injection say that he raised his left arm and calmly waited for the injection. His remains were cremated on 15 August, the feast day of the Assumption of Mary.