After the network was infiltrated and betrayed, Balachowsky was arrested and ultimately imprisoned at the Buchenwald Concentration Camp outside Weimar, Germany.
Sent to Camp Dora on 1 February 1944, he was brought back to Buchenwald May 1 of the same year to work developing a vaccine for typhus.
He also went to work helping the various underground groups inside the camp and established a network of contacts who fed him information from the camp's commanders.
Along with Eugen Kogon, Balachowsky was instrumental in the survival of several British SOE officers who were among a group sent to Buchenwald for execution.
It is also believed that Balachowsky had a hand in getting 168 imprisoned Allied airmen including Phil Lamason out of Buchenwald and into the hands of the German Luftwaffe just days before they were set to be executed.
After the war, Balachowsky testified at the Nuremberg Trials.