Eccarius was captured by the British and then handed over to the Soviets. He was put on trial for war crimes in 1947 by the Soviets in the Berlin Pankow city hall along with fellow SS guard and Sachsenhausen record keeper Gustav Sorge, the last Sachsenhausen commandant, Anton Kaindl, 11 other SS officers, one civil servant and two prisoner kapos including Paul Sakowski, who served as the crematorium foreman and camp hangman from 1941 to 1943.
Eccarius was found guilty on October 31, 1947 and was sentenced to life imprisonment with compulsory forced labor at the VorkutaGulag.
In January 1956, in a deal brokered by West German prime minister Konrad Adenauer, he along with other German prisoners of war were repatriated to West Germany and initially received amnesty. In 1962, he was indicted by the West German authorities for the shooting of prisoners near Wittstock, Germany while on a death march from Sachenhausen northwest to Crivitz, Germany begun on April 21, 1945 one day prior to liberation of the camp by the Soviet Army. He was found guilty on November 30, 1962 in the Federal District Court in Coburg, West Germany and sentenced to four years.
Additional criminal charges were filed against Eccarius in 1962 for complicity in the killing of over 13,000 Soviet prisoners in the "Genickschussanlage" (neck shooting facility) in 1941. The trial was held in the Federal District Court of Munich, where he was found guilty and sentenced to eight and a half years imprisonment on December 22, 1969. He was released after serving two years. He was also investigated for the murder of Yakov Iosifovich Dzhugashvili, son of Josef Stalin.