The "bunker" was a prison within a prison. Here were brought prisoners who had ostensibly contravened camp regulations and also those who had been condemned to death and awaited their execution. The incarceration alone in darkened cells with beatings and no food was the most terrible form of torture in the camp. The "bunker" was also the place of execution. Here the SS murdered camp inmates who had been declared "guilty" of some offence. They were accorded "special treatment" which in the end spelt death.

In the last months before liberation, up to 90 people were executed daily in the prison yard. A reasonable estimate is that between April 1944 and April 1945 more than 1500 death sentences were carried out here. For this purpose six new gallows hooks were installed and a firing squad wall was erected.

Among those executed were some who had never been prisoners in Flossenbuerg, but had been sent here expressly for this purpose: civilians as well as prisoners of war (for example, downed allied pilots, commissars of the Red Army), slave labourers, resistance groups (such as participants in the Warsaw Uprising or Czech resistance fighters from Bruenn with their families) and German army officers from the circle of those who tried to kill Hitler on July 20, 1944. Seven members of this plot were executed in Flossenbuerg between April 9 and 12, 1945: Admiral Wilhelm Canaris; Major General Hans Oster; the army judge, Dr. Karl Sack; Captain in the Intelligence, Ludwig Gehre; Pastor Dietrich Bonhoeffer; General Friedrich von Rabenau; and Reserve Captain Dr. Theodore Struenck.

In the "bunker" a number of British and French officers were kept in strictest isolation and cruelly tortured. All but one were hanged in Flossenbuerg on March 29, 1945.

In the final months arrived the so-called "special prisoners" and "prisoners of honour of the Fuehrer". Among the "prisoners of honour" were the former Hungarian Home Secretary, Franz Keresztes-Fischer, and his brother, Ludwig, a Hungarian General; the chief of the political police in Budapest, Josef Sombor, and a further eight prominent colleagues of his; and officers including one Czech, one Russian, two Italian and three French, generals.