After the evacuation of Auschwitz, Höcker was reassigned with Baer in January 1945 to the Dora-Mittelbau concentration camp. He used false papers to flee the camp and avoid being identified by the British when they captured him.
He married before the war and had a son and daughter during the war, with whom he was reunited after his release from a POW camp in 1946. Early in the 1960s he was apprehended by West German authorities in his hometown, where he was a bank official.
At his trial in Frankfurt, Höcker denied having participated in the selection of victims at Birkenau or having ever personally executed a prisoner. He was proved to have knowledge of the genocidal activities at the camp, but could not be proved to have played a direct part in them. He was imprisoned for aiding and abetting over 1,000 murders, but was released in 1970 and was able to return to his bank post as chief cashier.
In 2006, a photo album created by Höcker came to the attention of the United States Holocaust Memorial Museum; the album contains rare images of the life of German functionaries at Auschwitz while the camp remained in operation, including some of the few photos of Josef Mengele at Auschwitz.