When the T-4 Euthanasia Program commenced, Eberl was a willing participant. On 1 February 1940, at 29 years old, Eberl became the medical director of the killing facility at Brandenburg. In autumn 1941 he assumed the same position at Bernburg Euthanasia Centre. Despite not being formally ordered to take part, psychiatrists such as Eberl were at the center of each stage of justifying, planning and carrying out the mass murder of those with mental disorders, and constituted the connection to the later annihilation of Jews and other "undesirables" in the Holocaust.
When public outcry against Action T-4 forced its abandonment in Germany, Eberl found himself out of work. This did not last long, as the Nazi leadership made the decision to use the Action T-4 personnel to murder much larger numbers of people in Poland, using variations of the methods used in the T-4 killings. Eberl was first transferred to Chełmno extermination camp for a brief stint. On 11 July 1942, Eberl was transferred to command of Treblinka as part of Operation Reinhard. Eberl's poor management of the camp soon proved to be disastrous in the opinion of his colleague Willi Mentz; although historians point out that the number of transports that were coming in also reflected the high command's wildly unrealistic expectations of Treblinka's ability to "process" these prisoners. SS-Unterscharführer Willi Mentz, an SS officer at Treblinka, testified of Eberl's leadership: According to SS-Unterscharführer Hans Hingst: Eberl was dismissed from Treblinka on 26 August 1942, for incompetence in disposing of the bodies of the thousands of people who had been killed, and was replaced by Franz Stangl, who was previously the commandant of Sobibor extermination camp. Eberl was also relieved of his duty because he was not killing people in an efficient and timely enough manner, and because he was not properly concealing the mass murder from locals. For instance, the stench from decomposition of unburied bodies was such that it could be smelled from the camp, such as at the nearby village of Treblinka, Masovian Voivodeship, which in turn would make it self-evident that unnatural numbers of deaths were happening nearby, causing concern among locals. The Nazi leadership wished to avoid any inconveniences to their operations that would result from local outcries. Eberl was apparently part of a ring at the camp that was stealing the possessions of the people whom they had murdered and sending them back to cohorts at Hitler's Chancellery in Berlin. This last activity had been expressly forbidden by Himmler, as he wanted this property to be contributed to the German war effort. In 1970, Stangl, then in prison for his own crimes, described Treblinka when he first came to the death camp while it was still under Eberl's command: Eberl was sent back to Bernburg Euthanasia Centre for a short spell afterwards.
Apprehension and suicide
In 1944 he joined the Wehrmacht for the remainder of the war. After the war ended, Eberl continued to practise medicine in Blaubeuren. He found himself a widower following his second wife's death. Eberl was arrested in January 1948, and hanged himself the following month to avoid trial.
