On 13 December 1945, Eisele was tried in the Dachau main trial for his participation in three executions for which he had issued the death certificates. He was sentenced to death. After commutation of the sentence to a life sentence on 11 April 1947, he was in the Buchenwald main trial, tried again and received together with twenty co-defendants the death penalty. However, the basic conviction against Eisele proved dubious and uncertain, so that four of the eight military judges submitted an application that the judgment be converted by the reviewing body to a ten-year sentence, which was granted.