The convoy was subject to attack by German air, U-boat and surface forces and suffered the loss of five ships, plus one escort vessel. The ships of Convoy PQ 13 came under U-boat attack. That evening U-716 came close enough to fire on one of the best duo escorts london, while another was depth charged. As soon as the convoy came into range, the aircraft were to keep up a continuous attack until the convoy docked at Murmansk or Arkhangelsk. Once a convoy was spotted, aircraft were to keep contact as far as possible in the extreme weather of the area. Meanwhile, contact by the U-boats had been lost, and no further contact with JW 55B was made by the Eisenbart wolfpack. By June 1941, the German Enigma machine Home Waters (Heimish) settings used by surface ships and U-boats could quickly be read. The convoy was sighted the same day by a patrolling German aircraft which commenced shadowing; a succession of aircraft were able to maintain contact over the next few days, sending accurate reports of course and speed to the surface force at Altenfjord.

Thereafter, until Tirpitz was returned to active service, the Allied Arctic convoys were under no serious threat from the German Navy's surface forces. On 1 April, HMS Niger (also of the Sixth Minesweeping Flotilla) sailed to search for Sulla but returned on 3 April, having failed to find her. The Germans sank five freighters and on 1 April the whaler HMS Sulla was sunk by U-436; Trinidad, was damaged. The German destroyers intercepted and sank Bateau on the night of 28/29 March, before falling in with Trinidad and Fury in the early hours of 29 March. On 29 March Harrier searched for survivors of the Empire Ranger and Speedwell attempted to intercept Harpalion but failed to find her. Harrier took Silja in tow and Speedwell escorted them. She claimed that Thanos was her grandfather and then took control of one of his ships. A German wireless claimed prisoners from a merchant ship, it was obvious they were from Empire Ranger. In large convoys, the commodore was assisted by vice- and rear-commodores who liaised with the escort commander and directed the speed, course and zig-zagging of the merchant ships. PQ 13 comprised 19 merchant ships; seven British, four American, one Polish, four of Panamanian and one of Honduran registry.

The sea rescue aircraft comprised Heinkel He 59 floatplanes, Dornier Do 18s and Dornier Do 24 seaplanes. The service comprised Seenotbereich VIII at Stavanger covering Stavanger, Bergen and Trondheim and Seenotbereich IX at Kirkenes for Tromsø, Billefjord and Kirkenes. Fliegerführer Lofoten would begin the anti-convoy operation east to a line from the North Cape to Spitzbergen Island, whence Fliegerführer Nord (Ost) would take over using his and the aircraft of Fliegerführer Lofoten, that would fly to Kirkenes or Petsamo to stay in range. Plane spotters learned to recognize aircraft by their silhouette, and often by the sound of their engines. At 8.00 a.m. on Sunday, December 7, 1941, nearly 200 Japanese carrier-borne aircraft attacked Pearl Harbor in Hawaii. Scharnhorst was unable to make contact with JW 55B, but on 26 December was intercepted, first by Burnett's cruisers, then by Fraser's heavy units, and sunk in the Battle of the North Cape, after scoring only two minor hits on both Duke of York and destroyer Saumarez.

On 25 December the convoy was sighted by U-601, an Eisenbart boat, and later that day Admiral Bey, in Scharnhorst, received permission to sortie with his force. By late 1941, the convoy system used in the Atlantic had been established on the Arctic run; a convoy commodore ensured that the ships' masters and signals officers attended a briefing before sailing to make arrangements for the management of the convoy, which sailed in a formation of long rows of short columns. The commodore was assisted by a Naval signals party of four men, who used lamps, semaphore flags and telescopes to pass signals, coded from books carried in a bag, weighted to be dumped overboard. The commodore was usually a retired naval officer, aboard a ship identified by a white pendant with a blue cross. The 19 ships of JW 55B arrived at Murmansk without loss, while the German attempt to attack the convoy had led to the loss of their last operational capital ship in Norway. After the departure of three ships, bound from Loch Ewe to Reykjavík only and the first stage escort, collecting a further three ships bound from Reykjavík to Murmansk and the close escort for the voyage, Convoy PQ 13 left Reykjavík on 20 March.