Unlike her sisters, Admiral Scheer was not available to be staged in the Atlantic when war became imminent. She was at Wilhelmshaven at the start of the war, due for a major refit after service off Spain, and was slightly damaged in one of the first RAF attacks of the war. This damage was quickly repaired, but there were supply chain problems that delayed the start of the refit work. Hampered by mechanical problems, the ship was limited to short cruises in the local area until her refit began in April, 1940.

After the initial wave of surface raiders, which included the panzerschiffe Graf Spee and Deutschland, there had been a lull in raiding activity while the German Navy put all available resources into preparations for the invasion of Norway. But a second wave of raiders was planned for 1940, to include Admiral Scheer.

Just before the Norway operation, two armed merchant raiders put to sea. As the names of these vessels were changes many times while they were at sea to confuse Allied intelligence, I will refer to the armed raiders by their name as they left port. Ship 16 (Atlantis) sailed on March 11, and Ship 36 (Orion) sailed on April 7. These two vessels were to lay low, and then to reveal themselves in mid-April, to pull Royal Navy warships away from the North Sea at the height of the Norway operation. Ship 36 captured her first prize April 24 in the North Atlantic, and Ship 16 her first on May 5 in the South Atlantic.

In May and June, Ship 21 (Widder), Ship 33 (Pinguin), and Ship 10 (Thor) sailed on raiding cruises. Between them, these five ship claimed nearly 300,000 tons of shipping between June and September, and more importantly, caused the Royal Navy considerable strain as it took extensive countermeasures in every ocean.

The pocket battleship Deutschland, now renamed Lutzow, was to have entered the Atlantic in this time period also, immediately following her participation in the seizer of Trondheim. But the ship developed mechanical problems, and while returning to Germany was torpedoed by a British submarine and extensively damaged. Scharnhorst was also damaged, and while leaving for a sortie into Icelandic waters in late June Gneisenau was also damaged by a submarine torpedo.

This left only the heavy cruiser Hipper available for raiding, and she was quite unsuitable, due to her unreliable machinery and excessive fuel consumption. She conducted one sweep in the area of the Barents Sea, without success. Only in the next year, after a number of tankers had been positioned in the Atlantic, would Hipper go raiding.

The armed merchant raider Ship 45 (Komet) sailed in August, traversing the northern sea around Siberia to raid in the Pacific.

Admiral Scheer's refit, and post-refit working up period, lasted until September, when the ship was declared ready for service. She sailed to Norway, ready to start a raiding cruise, but while still in Norwegian waters her engines developed a minor problem, and the ship returned for repairs. Under the command of Captain Theodor Kranke, who had commanded the ship for the previous year, she finally departed Gotenhafen on October 23, 1940, to wage commerce war against the British Empire.
Like all raider commanders, Captain Kranke, while under the overall guidance of the Naval High Command, had extensive leeway in choosing his areas of operation and his tactics. Like his counterparts on Graf Spee and Deutschland, he was directed to avoid actions with enemy warships, as even slight damage suffered far from home could easily lead to the eventual loss of the ship. Like before, there were a number of supply ships in the Atlantic to re-supply Admiral Scheer, though thanks to the efforts of the Royal Navy not as many as previously.

Scheer hugged the Norwegian coast and then cut across the Arctic, slipping through the Denmark Straits on October 31 without being detected by the British.

Loose in the North Atlantic, with enemy forces unaware of her mission, Admiral Scheer soon found good hunting. On the late afternoon of November 5 the raider's scout plane sighted a large, poorly escorted eastbound convoy. It was convoy HX-87, with 37 freighters bound for Britain from Halifax, and escorted only by the armed merchant cruiser HMS Jarvis Bay. Built for the passenger trade to Australia for the Aberdeen & Commonwealth line and taken over by the Admiralty in 1939, the 14,000-ton ship was armed only with seven turn of the century 6-inch guns. She was a match for a merchant raider, but not for any warship.

Captain Kranke decided to attack immediately, despite the rapidly approaching darkness. The Jarvis Bay bravely charged out to protect her convoy, dropping smoke floats to try and screen her charges, but Admiral Scheer made short work of her, and the merchant cruiser was sunk before she ever got her guns into range. Only sixty-five men of her brave crew of 255 were picked up by the Swedish freighter Stureholm.

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Scheer then pursued the scattering merchant ships, sinking five and damaging three before darkness allowed the others to escape. The ships sunk were the Maiden (7900 tons), Trewellard (5200 tons), Kenbame Head (5200 tons), Frenso City (4950 tons), and the armed freighter Beaverford (10000 tons), which put up a gallant fight also. None of Jervis Bay or Beaverford's shells hit Admiral Scheer.
The attack on convoy HX-87 paid dividends far in excess of the ships sunk or damaged. The British suspended all shipping on the North Atlantic for a full week, and the strength of the Royal Navy was further taxed, as the Admiralty ordered that all large convoys were to be escorted by a battleship or several cruisers.
Meanwhile, Kranke headed south to his chosen hunting grounds along the shipping lanes between the Azores and West Indies, refueling from the tanker Eurofeld on the 12th and replenishing his ammo and supplies from the Nordmark on November 14th.

He sank the Port Horbard (7450 tons) on November 24th, and the Tribesman (6200 tons) on December 1. On December 14, the Admiral Scheer again met up with the supply ship Nordmark, refueling and resupplying.

The German raider headed further South, hoping to find richer pickings in the South Atlantic. On December 18, Admiral Scheer captured the British refrigerator ship Duquesa (8651 tons) with 14.5 million eggs and 3000 tons of meat on board. This proves to be a valuable prize: The Duquesa was used to resupply the auxiliary cruisers Pinguin and Thor, and the supply ship Nordmark.

On December 26, at a rendezvous point codenamed "Andalusien" located at 15-degrees South 18-degrees West, Admiral Scheer met up with Thor, Pinguin, the tanker Eurofeld, and the captured Duquesa to again resupply from the prize. No enemy ships were encountered for over two weeks, but on January 17, 1941, the Norwegian tanker Sandefjord (8000 tons) was captured. A prize crew was put on board, and the ship was sailed to Bordeaux in occupied France. Three days later the Dutch steamer Bareveld (5600 tons) and the British freighter Stanpark (5200 tons) were sighted and sunk. After this, it was time to head back to point "Andalusien" for another meeting with Thor and the supply ship Nordmark. The captured Duquesa, provider of much welcomed meat and eggs to the German raiders, continued to supply Pinguin until February, when the fuel to run her refrigeration ran out, and she was finally sunk.

The hunting was poor in the South Atlantic once the presence of the raider was known to Britain, so Captain Kranke headed around South Africa to the Indian Ocean in search of prey. Admiral Scheer passed the Cape of Good Hope on February 3.

On February 14, Admiral Scheer meet with the auxiliary raider Atlantis, the war prizes Speybank and Letty Brovi, and the German freighter Tannenfels at position 13-degrees South, 64-degrees East, to resupply. On February 20, the Greek freighter Gregorios (2550 tons) was sunk at the northern end of the Mozambique Channel, and the British tanker Advocate (6700 tons) was captured and sailed for occupied France. The next day the freighter Canadian Cruiser (7200 tons) was sunk, and Admiral Scheer received orders to return home.

Heading back south, Admiral Scheer sank the Indonesian steamer Ranaupandiang (2550 tons). A few hours later, Admiral Scheer is sighted by the British light cruiser Glasgow, at 8 degrees 30 minutes South, 51-degrees 35 minutes East, but slips away from the British ship, which is en route to Singapore for repairs from torpedo hits suffered off Crete. British forces, including the carrier Hermes, the heavy cruisers Canberra, Australia, and Shorpshire, and the light cruisers Glasgow, Cape Town, and Emerald, search in vain for the German raider.

On March 3, Admiral Scheer once again passed the Cape of Good Hope, and on the night of March 9-10 meets at point "Andalusien" with the supply ship Nordmark and the merchant raiders Pinguin and Kormoran. Headed back to North, Admiral Scheer would resupply again from the German freighters Portland and Alsterufer, finally passing the Denmark Strait on March 27. Skirting the Arctic ice pack, north of Iceland, and hugging the Norwegian coast, Admiral Scheer reached Bergen March 30. On June 1 she docked at Kiel, having sunk 14 merchant ships, captured 2 tankers, and destroyed an armed merchant cruiser accounting for 113,223 tons, with another 3 ships totaling 27,844 tons damaged.