1863: three-year-old season
Macaroni began his season at Newmarket in April when he won a one-mile stakes race by three lengths. Although the event was not particularly important, it proved that the colt went well on the course and coped with the unusually hard ground. Two weeks later over the same course and distance he started at odds of 10/1 against eight opponents for the 2000 Guineas, for which the favourite was the French colt Hospodar. Ridden by Tom Chaloner, he won by half a length from Saccharometer. The defeat of the French horse, who finished unplaced, and the popularity of Macaroni's owner, led to his win being warmly received by the Newmarket crowd.
On 20 May, Macaroni was a 10/1 chance for the Derby at Epsom, with Lord Clifden starting the 4/1 favourite in a field of thirty-one. The race was run in difficult conditions with heavy rain and soft ground. Among the spectators was the Prince of Wales, who became the first member of the British Royal Family to attend the race since Prince Albert in 1840. The start of the race was delayed for almost an hour, owing to a record thirty-two false starts caused by horses breaking away or failing to line up correctly. The huge field led to good deal of bumping and roughness, with three horses either falling or being brought down. Chaloner held up Macaroni in the early stages, before moving into fifth place entering the straight. A furlong from the finish, Lord Clifden went into a clear lead and looked the likely winner, but Macaroni produced a strong late run to catch the favourite in the last strides and win by a head. Rapid Rhone finished well to take third place. Macaroni's victory was warmly received in Newmarket, where the church bells were rung in celebration. Naylor marked his success by donating £1,000 to charities in his native city of Liverpool.
In July, Macaroni ran the Drawing Room Stakes at Goodwood. He was made odds-on favourite despite a ten pound weight penalty and won easily from two opponents. At York in August, he took on older horses in the two-mile York Cup and won by four lengths from Clarissimus.
At Doncaster in September, Macaroni bypassed the St Leger and ran instead in the 2+1⁄2-mile Doncaster Cup. He took the lead entering the straight and held off the sustained challenge of The Oaks winner Queen Bertha to win by one and a half lengths. At Newmarket in October he walked over in the Select Stakes and was then retired to stud.