U-boat crews boarding merchant ships had been a common feature of the First Battle of the Atlantic, during WWI. The rules of war required anyone wishing to sink a neutral merchant ship to search it for contraband - enemy goods useful in times of war. If it was present, the crew had to be given warning that their ship was to be sunk, avoiding unnecessary loss of life. The boarding party could then, use explosives to sink the ship. This saved torpedoes, allowing the submarine to sink more ships; the ability to loot fresh provisions was a bonus. The problem was that it forced the U-boat to stay on the surface, an easy target for any hunting warships. It also exposed the submarine to fire if the merchant was armed, or was a disguised 'Q-ship'. To this end, the German Navy switched to 'unrestricted submarine warfare', where submarines could fire without warning or searching. In this mode, submarines tended to remain submerged, and to attack without warning. The Allied adoption of convoy in response to German actions enforced this change. There was no way for a submarine to force a merchant in convoy to stop; to attempt it would just bring down the escorts on the submarine's head.

The Second Battle of the Atlantic greatly resembled the latter part of the First Battle. Merchants travelled in convoys, and submarines attacked from hiding. However, there were still cases where merchant ships were boarded. During the early days of the battle, while ships were sailing alone as the convoy system was set up, there were several cases of ships being boarded. The most prominent of these is the case of the Fanad Head. This steamer was stopped by U-30, on the 14th September 1939. The crew and passengers abandoned ship, while U-30 sent across a two-man team to sink the ship with demolition charges, as well as searching the ship for papers, fresh vegetables, bread and other useful supplies. However, Fanad Head's radioman had managed to get off a signal warning of a submarine attack. The carrier Ark Royal responded to the distress signal, launching three Skua dive-bombers. The aircraft arrived while the demolition team were still aboard Fanad Head, forcing U-30 to dive and abandon them. The aircraft attacked the demolition team's boat (which had been left on the surface when U-30 dove), but two aircraft were destroyed by their own bomb blasts. Their pilots survived, and were rescued by the demolition team, while U-30 sank Fanad Head with torpedoes. Other cases came following America's entry to the war. The USN was unwilling to establish a convoy system along the Eastern Seaboard due to a lack of escorts. This made the American coastal traffic hugely vulnerable to submarines. In this target-rich environment, many U-boat captains ran low on torpedoes, and chose to send boarding parties to scuttle merchants instead. Finally, in July 1942, during the disastrous PQ17 convoy, the Dutch freighter Paulus Potter was damaged by German bombers, and abandoned. The hulk drifted for several days, before being encountered by U-255. U-255's crew boarded her, carrying away a number of secret papers and code books, as well as luxuries like cigarettes.

Merchant sailors did not carry marines armed to fight off boarders. The 'Merchant Marine' was simply another way of saying the Merchant Navy - in other words, everyone who manned merchant ships. Armed merchant ships could carry a military detachment to man their naval guns and AA weapons. In Britain, these were overseen by the DEMS (Defensively Equipped Merchant Ships) organisation. DEMS gunners were mainly drawn from the Army's Royal Artillery, as well as the Royal Navy and Royal Marine reserves. Members of the Merchant Navy (including at least one stewardess) were also trained as 'merchant seaman gunners'. The DEMS gunners had a complicated bureacratic existence; they had to sign on as members of the Merchant Navy, in addition to their service in any of the armed forces. Merchant sailors could surrender; it was fairly common practice for U-boat crews to pick survivors out of lifeboats for interrogation. The German Navy operated a prisoner of war camp for merchant seamen, Milag Nord, near Bremen (it was next door to its camp for Allied naval personnel, Marlag Nord, and the two are usually considered together).