In 1939, Witold decided to stay in the country and continue fighting the enemy. He joined an underground military organisation called the Polish Secret Army, which itself took orders from the Polish Government in Exile. Within the organisation, he served as Chief of Staff. On August of 1940, his direct commanders were arrested by the Nazis and sent to Auschwitz Concentration Camp. At the time knowledge of the concentration camps being set up in occupied Poland was very limited, therefore Witold was urged to get to Auschwitz and organise a Resistance movement inside. 

The goal of the Polish Underground State was to gather information about the concentration camps under construction, as well as to help the imprisoned and even organise a joint escape. Witold agreed, and in September 1940 he allowed the German forces to catch him in a raid, after which he was sent to Auschwitz. Witold hid under the false identity of Tomasz Serafiński and was given number 4859 in the camp.  

It became apparent very quickly that a prisoners’ uprising or a collective escape had no chance of success. Witold organised a Resistance movement whose tasks were to provide the Home Army with reports and mutual aid to the prisoners. For this reason, aid was organised for prisoners in the form of food and clothing, and lighter labour was arranged. Members of the Resistance movement also had their eyes and ears wide open, collecting information about the Nazis’ criminal activities.  

The Resistance reports that Witold handed over to the Polish Underground State were the first testimonies about the Holocaust during World War II. Witold himself created the reports, which were later transmitted in their entirety to the western European countries. In the report, Pilecki wrote: 

What can mankind say today, this mankind that wants to prove the progress of culture, and to place the 20th century much higher than the centuries past? Can we, the people of the 20th century, at all look into the faces of those who lived in the past and prove our superiority, when in our time the armed mass destroys not enemy armies, but entire nations, defenseless societies, using the latest technological achievements.

Witold, threatened with deconspiration (being found out), escaped from Auschwitz and fought in the Polish Resistance movement until the end of World War II. After the war, he was tortured and murdered in 1948 by the Communists, and was remembered as a criminal by the authorities until the fall of Communism in Poland. It was not until 50 years after his death that his memory was rehabilitated.