While Dönitz was fanatical for his support of the Hitler and having the Kriegsmarine committed to National Socialist values, there was very little for the IMT to pin on him. There were four main charges for the IMT : conspiracy for a crime against peace, waging wars of aggression, war crimes, and crimes against humanity. Count I (conspiracy) was one of the more serious counts for the service chiefs brought to trial. Dönitz here had the advantage of not having been the head of the Kriegsmarine during German rearmament. His superior until 1943, Erich Raeder, did receive that charge and the Tribunal found him guilty. This left the prosecution to charge Dönitz with prosecuting the war in an inhumane manner and responsibility for various war crimes. The nature of the German naval war meant that these charges largely focused on the actions of u-boat crews. Here there was enough ambiguity that Dönitz's defense team was able to capitalize upon. In a reversal of its position, the Tribunal allowed a de facto tu quoque defense when Dönitz's defense team provided an affidavit from USN Admiral Nimitz that the US engaged in unrestricted submarine warfare and was justified in doing so. Nimitz's affidavit contended that the Allies interpreted the legality of unrestricted submarine warfare much the same way as the Germans. Dönitz's responsibility for unrestricted submarine warfare was one of the centerpieces for the prosecution's strategy. This left the prosecution with Dönitz's support for the Commando Order, connections with Hitler's proposal to scrap the Geneva Conventions, and his knowledge of slave labor in German shipyards to charge him with. Although he was guilty of these counts, there was enough ambiguity surrounding his direct culpability to warrant a milder sentence.

As far as his liability as head of state, he held office for a very short time and his main action was to negotiate the surrender. As such, he wasn't held responsible for specific German war crimes, such as the concentration camps.

The main charge against him as commander of the U-Boat force, and later as the Commander-in-Chief of the Navy, was that he waged unrestricted submarine warfare. In particular, he ordered the U-Boats not to stop to allow crew and passengers of merchant vessels to evacuate before attacking (War Order 154). He later ordered the U-Boats not to attempt to rescue survivors, after the Laconia incident in which U-Boats rescuing survivors of the RMS Laconia were attacked by Allied aircraft. These orders were deemed to be in violation of Article 22 of the First London Naval Treaty.

However, US and British naval officers testified at Doenitz's trial that both countries had issued similar orders, particularly the US unrestricted submarine warfare in the Pacific. Sentencing Doenitz those charges would have proved embarrassing to the Allies. He was convicted and sentenced of more general war crimes and of planning and conducting a war of aggression.