The ship thereafter resumed training duties in the Baltic Sea. These lasted with minor interruptions until September 1941, when she was assigned to the Baltic Fleet and tasked with supporting German operations during the invasion of the Soviet Union. Training duties resumed in 1942 and lasted until late 1944, when she took part in minelaying operations in the Skagerrak. Damaged in a grounding accident in December 1944, she went to Königsberg for repairs. In January 1945, she participated in the evacuation of East Prussia to escape the advancing Soviet Army. While undergoing repairs in Kiel, "Emden" was repeatedly damaged by British bombers and later run aground outside the harbor to prevent her from sinking. In the final days of the war, she was blown up to prevent her capture. The wreck was ultimately broken up in place by 1950.