In 1940 he presented his plan to enter Auschwitz to gather intelligence and organize inmate resistance. His superiors provided him with a false identity: Tomasz Serafiński. On September 19, during a Warsaw street roundup, he was caught, detained for two days, then sent to Auschwitz and assigned prisoner number 4859. Pilecki organized the underground Union of Military Organizations (ZOW) at Auschwitz, and many smaller organizations at Auschwitz eventually merged with it. ZOW improved inmate morale, provided news from outside, distributed extra food and clothing to members, set up intelligence networks, and trained detachments in the event of a relief attack by the Home Army, arms airdrops, or airborne landing by the Polish First Independent Parachute Brigade, based in Britain. ZOW provided the Polish underground with information about the camp and sent reports to Warsaw starting in October 1940. Beginning in March 1941, the Polish resistance forwarded those reports to the British government in London. When the organization began, Pilecki organized its members into cells of five, so each member was in communication with only four others. If one member was caught, this limited the number of men he could potentially expose under torture.

Pilecki worked in various kommandos, including carpentry, a weaving workshop, the tannery, and the parcel office. In 1942 Pilecki’s resistance movement used a radio transmitter to broadcast arrivals, deaths, and inmate conditions, then dismantled it that autumn, fearing the Germans might discover it. Through civilian workers, Pilecki sent out coded messages and obtained medicine and typhus vaccines. He hoped that either the Allies would drop arms or troops into the camp, or the Home Army would organize an assault; meanwhile, the camp Gestapo under SS-Untersturmführer Maximilian Grabner captured and killed many ZOW members.

Pilecki decided to break out of the camp and personally convince the Home Army leaders that a rescue attempt was possible. After a clever plan involving faking a case of typhus and getting himself transferred to the bakery kommando, Pilecki and a few inmates enacted their escape on the evening of Easter Monday in 1943. At the bakery in town, they changed into civilian clothes provided by friends, took the back door off its hinges, and ran, carrying powdered tobacco to hide their scent from SS tracking dogs. While sheltering with a trusted contact, Pilecki contacted his Warsaw connections, saying he would remain near Auschwitz and form a detachment while he waited for permission to attack the camp; however, if his plan was denied and he was ordered to desist, he would return to Warsaw. In July, the Home Army commander was arrested, so Pilecki realized he wouldn’t get an answer yet. He went to Warsaw and exchanged letters with men in Auschwitz to keep up their spirits. In the fall of 1943, he presented his full plan of attack and wrote his final Auschwitz report. In 1944, he took part in the Warsaw Uprising. Despite his efforts, the Home Army did not have enough manpower to successfully attack Auschwitz.