In 1787 he was appointed Major of a new battalion at Chatham, and he gladly forsook civil for military duties. During the following year he rejoined his first regiment, the 51st, at Cork, and soon became Lieutenant-General. While he was there young Anderson, an Ensign in his regiment, became one of his most devotedly-attached friends, and was ever after his inseparable companion.
By this time he was known as a disciplinarian of unusual power, indulgent when he might safely be so, but inflexible in enforcing strict obedience. In an age when hard drinking was the fashion, he set his face like a flint against habits of intemperance, alike in the ranks and among officers, from most of whom he had steady support. One young lieutenant, who ventured to appear on parade in a state of intoxication, was forced by him to resign the service, and from that time Moore had no further trouble. His regiment became widely known for its exceptional sobriety and dependableness.
In 1792 he was ordered to Malta, and two years later he was fighting with the French in Corsica, the peace having already come to an end. On the 10th of July ended successfully the siege of Calvi, that being the last spot in the island which the French had managed so far to keep. As Moore was gallantly storming the breach he had a severe wound, a fragment of shell striking him on the head. For an instant he was stunned; but regaining sense, he once more sprang up the breach. Sir Charles Stuart, chief-in-command, looking anxiously on, was alarmed at the bursting of shells among the assailants. He rushed forward and dashed over intervening obstacles, to find Moore in the midst of shouting grenadiers, his face streaming with blood. Apparently the great dread of Sir Charles had been that he was killed, for in the excitement of the moment he caught him in his arms, hardly able to utter his thankfulness, not only that the breach was won, but that John Moore still lived.
Two years later a collision between the English viceroy of Corsica, Sir Gilbert Elliot, and Sir Charles Stuart, made the latter resign his command and return to England; and later Moore was sharply ordered home by Elliot, who seems to have been annoyed with the friendship between him and the leading Corsican patriots. Moore, on reaching England, protested with much heat against the way in which he had been treated. He had, however, no need to disquiet himself. The King and the Duke of York took the matter up, promoted him to the rank of Brigadier-General, and sent him out to the West Indies, there to serve under Abercrombie. Both the Duke of York and Pitt had been, from the time of his seat in Parliament, his personal friends. Wherever he went he made friends for life.