From 7 November to 15 February 1941, the ship was in dry dock for maintenance. In September, she was assigned to the Baltic Fleet, centered on the newly commissioned battleship ; the Baltic Fleet was tasked with preventing the Soviet Navy from breaking out of the Baltic. "Emden" and "Leipzig" were the core of the southern group, which was based in Libau. The fleet remained on station only briefly, and when it became clear that the Soviet fleet had remained in port, the German Baltic Fleet was dissolved. On 16 September, "Emden" was operating off Dagö with "Leipzig" and three torpedo boats; the ships came under fire from Soviet coastal batteries, but were undamaged. A group of four Soviet torpedo boats also made an unsuccessful attack on the German squadron. "Emden" again provided gunfire support to German troops fighting on the Sworbe Peninsula from 26 to 27 September. Later on the 27th, the ship was transferred to Gotenhafen. She was assigned to the newly formed Training Unit of the Fleet in November 1941, and she would remain attached to the unit for the rest of the war. From June to November 1942, the ship was thoroughly overhauled in Wilhelmshaven, before returning to Gotenhafen on 7 November. Raeder again came aboard the ship for the voyage back to Gotenhafen; this was his last visit to a warship before his resignation.