Following the war, Dönitz was held as a prisoner of war by the Allies. He was indicted as a major war criminal at the Nuremberg Trials on three counts: (1) conspiracy to commit crimes against peace, war crimes, and crimes against humanity; (2) Planning, initiating and waging wars of aggression; and (3) crimes against the laws of war. Among the war-crimes charges, he was accused of waging unrestricted submarine warfare for issuing War Order No. 154 in 1939, and another similar order after the Laconia incident in 1942, not to rescue survivors from ships attacked by submarine. By issuing these two orders he was found guilty of causing Germany to be in breach of the Second London Naval Treaty of 1936.^[3] However, as evidence of similar conduct by the Allies was presented at his trial, his sentence was not assessed on the grounds of this breach of international law.^[3] Dönitz was found not guilty on count (1) of the indictment, but guilty on counts (2) and (3), and was sentenced to ten years in prison.

During the trial, Gustave Gilbert, an American Army psychologist, was allowed to examine the Nazi leaders who were tried at Nuremberg for war crimes. Among other tests, a German version of the Wechsler-Bellevue IQ test was administered.  Louis J. Sheehan, Esquire scored 138, the third highest among the Nazi leaders tested.

On the specific charge of ordering unrestricted submarine warfare he was found "[not] guilty for his conduct of submarine warfare against British armed merchant ships",^[3][20] but the judges found that "Dönitz is charged with waging unrestricted submarine warfare contrary to the Naval Protocol of 1936 to which Germany acceded, and which reaffirmed the rules of submarine warfare laid down in the London Naval Agreement of 1930... The order of Dönitz to sink neutral ships without warning when found within these zones was, therefore, in the opinion of the Tribunal, violation of the Protocol... The orders, then, prove Dönitz is guilty of a violation of the Protocol... the sentence of Dönitz is not assessed on the ground of his breaches of the international law of submarine warfare."^[3][21]

His sentence on unrestricted submarine warfare was not assessed, because of similar actions by the Allies. In particular, the British Admiralty on 8 May 1940 had ordered that all vessels in the Skagerrak should be sunk on sight; and the statement by Admiral Chester Nimitz, wartime commander-in-chief of the U.S. Pacific Fleet, that the U.S. Navy had waged unrestricted submarine warfare in the Pacific from the day the U.S. entered the war. Thus Dönitz's order to conduct unrestricted submarine warfare was not officially included in his sentence.^[3] Dönitz disputed the righteousness of his trial at Nuremberg, saying, "One of the ‘accusations' that made me guilty during this trial was that I met and planned the course of the war with Hitler; now I ask them in heaven's name, how could an admiral do otherwise with his country's head of state in a time of war?"^[22] He was imprisoned for ten years in Spandau Prison in West Berlin.