Atheltemplar returned to Great Britain with Convoy HG 9 which left Port Said on 19 November 1939, but on the afternoon of 14 December 1939, she struck a mine laid by German destroyers off the Tyne Estuary.

During late May and early June 1940 she was involved in Operation Dynamo, during which she bunkered Royal Navy destroyers and was attacked by the Luftwaffe several times in and around Dover Harbour.

Atheltemplar then made a series of coastal voyages in home waters before undergoing refit in Smith's Yard, North Shields in the winter of 1940–41.

The remains of five unidentified members of her crew ("Known only unto God"), killed during the 1 March 1941 air attack, lie within a marked Commonwealth War Grave towards the south-east corner of New Calton Burial Ground in Edinburgh, about 2 miles (3 km) south of Port Leith.

Later in the Second World War Atheltemplar was used on convoys to carry fuel oil and supplies to the Kola Inlet and the northern Soviet ports of Arkhangelsk and Murmansk.

This Convoy was attacked by German destroyers, U-boats and torpedo bombers; once again Atheltemplar was damaged but it is not clear whether the cause was ice, enemy action or both.

After reaching Iceland on 7 May 1942, Atheltemplar then returned to North Shields for repairs (and possibly for the fitment of additional anti-aircraft defensive armament).

A series of U-boat alerts followed, and then at about 1500 a large formation of He 111s and Ju 88s of KG26 attacked with bombs and at least 30 torpedoes; eight of the convoy's ships were sunk.

The master, 42 crew members and 18 gunners were picked up by the British rescue ship Copeland and the O-class destroyer HMS Offa.

Then, at 14.30 hours, U-408 came across the capsized wreck of the Atheltemplar, by now drifting north of Bear Island,[3] and sank her with her 88 mm gun at position 76°00′N 18°00′E / 76.000°N 18.000°E / 76.000; 18.000.

By the time of her sinking, Atheltemplar had completed at least 19 wartime Atlantic crossings, had sailed some 102,500 miles, and delivered 140,200 tons of essential fuel oil and molasses.