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In September 1939, Poland was invaded by the German Nazis.  Kolbe, who had already openly criticized Nazism and Communism, quickly sent away most of his friars, lest they, too, be arrested, as he suspected the Gestapo would do to him.  Kolbe and the remaining friars were jailed, however in December, they were unexpectedly released and allowed to return to Niepokalanow. 

Kolbe proceeded to set up the monastery as a refugee camp for three thousand people targeted by the Nazis, two thirds of whom were Jewish. All of the refugees were assigned jobs and for a short while, they worked as a highly efficient little community.  The next year, Kolbe was permitted to resume printing of the magazine, but shortly after, in February, he was arrested again and taken to Pawiak Prison after Kolbe made a reference to the war considered anti-Nazi in his magazine.

 In May, he was transferred to Auschwitz and branded prisoner #16670.  Despite being often singled out for beatings and ridicule by the guards, Kolbe worked diligently at his job of constructing the crematorium and remained calm.  Unlike some other inmates, he did not turn bitter and found solace in his faith.  One prisoner recalled him saying to some others "... these Nazis will not kill our souls ... when we die, then we die pure and peaceful, resigned to God in our hearts."  Kolbe was a positive and uplifting influence on the people he was detained with.  He regularly and readily conducted mass, lead prayers, distributed Communion, hear confessions and discussed Mary or other aspects of Christian theology.

Sometimes he had to cut and carry huge tree trunks under the direction of a former criminal called Krott, who particularly loathed Kolbe and made a game out of testing how much harsh treatment he could resist.  One day, after being forced to run with the weight of several large planks on his back, Kolbe collapsed and rather than being rushed to the camp hospital, was kicked in the face and stomach by Krott before being left lying in the mud, unconscious and on the verge of death.  Kolbe's life would have ended there and then were it not for the goodwill of some of his friends, who took him to the camp hospital.