Schongarth was born in 1903 in the town of Leipzig. He became a member of the SD Sicherheitdienst Intelligence Service of the SS Schutzstaffel in 1933. He later became the SIPO Sicherheitspolizei Security Police head in Government General. He was then appointed Commander of the Gestapo in the Netherlands.
During the time he was stationed in Krakow, Poland, he formed an Einsatzgrupen Special Action Group. He was responsible for the murder of up to 4,000 Jewish citizens between July and September of 1941.
Schongarth was captured at the end of the war. He was found guilty of executing a downed Allied pilot (which occurred on November 21, 1944) by a British Court in Burgsteinfurt on February 11, 1946. He was executed on May 16, 1946.