In August 1755 he followed Keppel to the Swiftsure, and in January 1756 to the Torbay, in which he continued till his promotion to commander's rank on 21 September 1759, and during this time was present in the expedition to Basque Roads in 1757, at the reduction of Gorée in 1758, and in the blockade of Brest in 1759, up to within two months of the battle of Quiberon Bay, from which his promotion just excluded him.
From October 1759 to April 1760 he had command of the Royal Exchange, a hired vessel employed in petty convoy service with a miscellaneous ship's company, consisting to a large extent of boys and foreigners, many of whom (he reported) could not speak English, and all impressed with the idea that as they had been engaged by the merchants from whom the ship was hired they were not subject to naval discipline. It would seem that a misunderstanding with the merchants on this point was the cause of the ship's being put out of commission after a few months.
As a commander Duncan had no further service, but on 25 February 1761 he was posted and appointed to the HMS Valiant, fitting for Keppel's broad pennant. In her he had an important share in the reduction of Belle Île in June 1761, and of Havana in August 1762. He returned to England in 1763, and, notwithstanding his repeated request, had no further employment for many years.
During this time he lived principally at Dundee, and married on 6 June 1777 Henrietta, daughter of Robert Dundas of Arniston, Lord President of the Court of Session. It would seem that his alliance with this influential family obtained him the employment which he had been vainly seeking during fifteen years. Towards the end of 1778 he was appointed to HMS Suffolk, from which he was almost immediately moved into HMS Monarch. In January 1779 he sat as a member of the court-martial of Keppel, and in the course of the trial interfered several times to stop the prosecutor in irrelevant and in leading questions, or in perversions of answers. The admiralty was therefore desirous that he should not sit on the court-martial of Sir Hugh Palliser, which followed in April, and the day before the assembling of the court sent down orders for the Monarch to go to St. Helens. Her crew, however, refused to weigh the anchor until they were paid their advance; and as this could not be done in time, the Monarch was still in Portsmouth harbour when the signal for the court-martial was made; so that, sorely against the wishes of the admiralty, Duncan sat on this court-martial also.
During the summer of 1779 the Monarch was attached to the Channel fleet under Sir Charles Hardy; in December was one of the squadron with which Rodney sailed for the relief of Gibraltar, and had a prominent share in the action off St. Vincent on 16 January 1780. On returning to England Duncan quit the Monarch, and had no further command till after the change of Ministry in March 1782, when Keppel became first lord of the admiralty. He was then appointed to HMS Blenheim of 90 guns, and commanded her during the year in the Grand Fleet under Howe, at the relief of Gibraltar in October, and the rencounter with the allied fleet off Cape Spartel. He afterwards succeeded Sir John Jervis in command of the Foudroyant, and after the peace commanded HMS Edgar as guardship at Portsmouth for three years. He attained flag rank on 24 September 1787, became Vice Admiral 1 February 1793, and Rear Admiral 1 June 1795. In February 1795 he was appointed commander-in-chief in the North Sea, and hoisted his flag on board HMS Venerable.
The situation was one of extreme difficulty, for the mutiny which had paralysed the fleet at the Nore broke out also in that under Duncan, and kept it for some weeks in enforced inactivity. Duncan's personal influence and some happy displays of his vast personal strength held the crew of the Venerable to their duty; but with one other exception, that of the Adamant, the ships refused to quit their anchorage at Yarmouth, leaving the Venerable and Adamant alone to keep up the pretence of the blockade.
Fortunately the Dutch were not at the time ready for sea; and when they were ready and anxious to sail, with thirty thousand troops, for the invasion of Ireland, a persistent westerly wind detained them in harbour till they judged that the season was too far advanced. For political purposes, however, the French Revolutionaries who controlled the government in Holland, in spite of the opinion of their admiral, De Winter, to the contrary, ordered him to put to sea in the early days of October.
Duncan, with the main body of the fleet, was at the time lying at Great Yarmouth revictualling, the Texel being watched by a small squadron under Captain Henry Trollope in HMS Russell, from whom he received early information of the Dutch being at sea. He at once weighed anchor, and with a fair wind approached the Dutch coast, saw that the fleet was not returned to the Texel, and steering towards the south sighted it on the morning of 11 October about seven miles from the shore and nearly halfway between the villages of Egmont and Camperdown. The wind was blowing straight on shore, and though the Dutch forming their line to the north preserved a bold front, it was clear that if the attack was not made promptly they would speedily get into shoal water, where no attack would be possible. Duncan at once realised the necessity of cutting off their retreat by getting between them and the land. At first he was anxious to bring up his fleet in a compact body, for at best his numbers were not more than equal to those of the Dutch; but seeing the absolute necessity of immediate action, without waiting for the ships astern to come up, without waiting to form line of battle, and with the fleet in very irregular order of sailing, in two groups, led respectively by himself in the Venerable and Vice-admiral Richard Onslow in the Monarch, he made the signal to pass through the enemy's line and engage to leeward.
It was a bold departure from the absolute rule laid down in the Fighting Instructions, still new, though warranted by the more formal example of Howe on 1 June 1794; and on this occasion, as on the former, was crowned with complete success. The engagement was long and bloody; for though Duncan, by passing through the enemy's line, had prevented their untimely retreat, he had not advanced further in tactical science, and the battle was fought out on the primitive principles of ship against ship, the advantage remaining with those who were the better trained to the great gun exercise, though the Dutch by their obstinate courage inflicted great loss on the English.
It had been proposed to De Winter to make up for the want of skill by firing shell from the lower deck guns; and some experiments had been made during the summer which showed that the idea was feasible; but want of familiarity with an arm so new and so dangerous presumably prevented its being acted on in the battle.
Duncan was awarded the Large Naval Gold Medal and an annual pension of £3,000, to himself and the next two heirs to his title - this was the biggest pension ever awarded by the British government. Additionally, he was given the freedom of several cities, including Dundee and London.
Till 1801 Duncan continued in command of the North Sea fleet, but without any further opportunity of distinction. Three years later, 4 August 1804, he died quite suddenly, aged seventy-three, at the inn at Cornhill, a village on the border, where he had stopped for the night on his journey to Edinburgh (ib. 252) and was buried in Lundie. He left a family of four daughters, and, besides the eldest son who succeeded to the peerage, a second son, Henry, who died a captain in the navy and K.C.H. in 1835.
Several ships have been named HMS Duncan after him, also a street in Leeds town centre is named after him (Duncan Street). The pub on this street honours him with its name and many pictures and paintings.
A statue of Duncan was erected in 1997 in Dundee, on the corner of High Street and Commercial Street. A gay pub in the Old Compton Street in London has the name of Lord Duncan.