The increasing frequency of Allied air attacks on the minelaying operations led to their cancellation in late October. For the rest of the year, she was occupied with escorting convoys in the Baltic. On 1 November 1944, Emden assisted the cruiser Köln, which had run aground. Emden herself ran aground in the Oslofjord on 9 December, though she was refloated the following day. She left Oslo on 23 December and steamed to Königsberg for repairs, arriving two days later. After entering the dry dock at the Schichau-Werke shipyard in Königsberg, her guns were removed and repair work began at a leisurely rate. She was there, still awaiting the completion of repairs when the Soviet Army attacked the city of Königsberg in January 1945, and on 23 January the naval high command ordered all naval forces in the city to evacuate. Emden had her guns reinstalled and she embarked the remains of Paul von Hindenburg and his wife, which had been disinterred to prevent them from falling into the hands of the advancing Soviet Army. She carried them to Pillau, under tow from several icebreakers, where they were transferred to the transport ship . In Pillau, Emdens engines were put back in working order, though she was only able to use one of her propellers. Emden then steamed as fast as was possible to Kiel, where she arrived on 6 February. There, she went into drydock at the Deutsche Werke shipyard for repairs. While in Deutsche Werke, Emden was under continuous air attacks. An air raid on 11 March set the forward deck and port side torpedo launchers on fire with incendiary bombs. Another attack on 3 April scored a direct hit on the ship's forward funnel, destroying it. On the night of 9–10 April, an Allied bombing raid severely damaged the ships in Kiel; the heavy cruisers and were both destroyed by bombs and Emden was slightly damaged by a near miss astern. Further, more serious damage was done on 13 April, and the next morning she was towed out into Heikendorfer Bucht. She had a 15 degree list to port, but the crew managed to stop the flooding and seal the hull. To prevent her from sinking, she was run aground in the shallows, and was decommissioned on 26 April 1945. To prevent her capture by the advancing Allied armies, her crew destroyed the ship with explosives on 3